diff --git a/pathways/WP1000/WP1000.gpml b/pathways/WP1000/WP1000.gpml index 5fa2677cc..5ce146340 100644 --- a/pathways/WP1000/WP1000.gpml +++ b/pathways/WP1000/WP1000.gpml @@ -287,21 +287,33 @@ - - 16258029 + + 3619897 PubMed - Epoxyeicosatrienoic and dihydroxyeicosatrienoic acids dilate human coronary arterioles via BK(Ca) channels: implications for soluble epoxide hydrolase inhibition. - Am J Physiol Heart Circ Physiol - 2006 - Larsen BT - Miura H - Hatoum OA - Campbell WB - Hammock BD - Zeldin DC + A novel pool of rat liver inositol and ethanolamine phospholipids contains epoxyeicosatrienoic acids (EETs). + Biochem Biophys Res Commun + 1987 + Capdevila JH + Kishore V + Dishman E + Blair IA Falck JR - Gutterman DD + + 14626496 + PubMed + Role of cytochrome P450-dependent arachidonic acid metabolites in liver physiology and pathophysiology. + Prostaglandins Other Lipid Mediat + 2003 + Sacerdoti D + Gatta A + McGiff JC + + + arachidonic acid metabolic pathway + PW:0000460 + Pathway Ontology + 2834948 PubMed @@ -313,26 +325,36 @@ Sacerdoti D McGiff JC - - 6548162 + + 10759591 PubMed - Biosynthesis of 5,6-dihydroxyprostaglandin E1 and F1 alpha from 5,6-dihydroxyeicosatrienoic acid by ram seminal vesicles. - Biochim Biophys Acta - 1984 - Oliw EH + Molecular mechanisms controlling nutritive blood flow: role of cytochrome P450 enzymes. + Acta Physiol Scand + 2000 + Harder DR + Roman RJ + Gebremedhin D - - 16399376 + + 4051502 PubMed - Nomenclature for mammalian soluble glutathione transferases. - Methods Enzymol - 2005 - Mannervik B - Board PG - Hayes JD - Listowsky I - Pearson WR + Novel glutathione conjugates formed from epoxyeicosatrienoic acids (EETs). + Arch Biochem Biophys + 1985 + Spearman ME + Prough RA + Estabrook RW + Falck JR + Manna S + Leibman KC + Murphy RC + Capdevila J + + metabolic pathway of secondary metabolites + PW:0000147 + Pathway Ontology + 17494091 PubMed @@ -345,27 +367,39 @@ Zeldin DC Wegmann M - - 14626496 + + 15748653 PubMed - Role of cytochrome P450-dependent arachidonic acid metabolites in liver physiology and pathophysiology. - Prostaglandins Other Lipid Mediat - 2003 - Sacerdoti D - Gatta A - McGiff JC + Epoxide hydrolases: their roles and interactions with lipid metabolism. + Prog Lipid Res + 2005 + Newman JW + Morisseau C + Hammock BD - - 3619897 + + 18383502 PubMed - A novel pool of rat liver inositol and ethanolamine phospholipids contains epoxyeicosatrienoic acids (EETs). - Biochem Biophys Res Commun - 1987 - Capdevila JH - Kishore V - Dishman E - Blair IA + Gerry Brooks and epoxide hydrolases: four decades to a pharmaceutical. + Pest Manag Sci + 2008 + Morisseau C + Hammock BD + + + 16258029 + PubMed + Epoxyeicosatrienoic and dihydroxyeicosatrienoic acids dilate human coronary arterioles via BK(Ca) channels: implications for soluble epoxide hydrolase inhibition. + Am J Physiol Heart Circ Physiol + 2006 + Larsen BT + Miura H + Hatoum OA + Campbell WB + Hammock BD + Zeldin DC Falck JR + Gutterman DD 16179585 @@ -385,6 +419,23 @@ Busse R Nilius B + + 3977905 + PubMed + On the metabolism of epoxyeicosatrienoic acids by ram seminal vesicles: isolation of 5(6)epoxy-prostaglandin F1 alpha. + Biochem Biophys Res Commun + 1985 + Oliw EH + Benthin G + + + 6548162 + PubMed + Biosynthesis of 5,6-dihydroxyprostaglandin E1 and F1 alpha from 5,6-dihydroxyeicosatrienoic acid by ram seminal vesicles. + Biochim Biophys Acta + 1984 + Oliw EH + 17164131 PubMed @@ -397,36 +448,6 @@ Jinks SL Hammock BD - - 18216721 - PubMed - Genetic variation in cytochrome P450 2J2 and soluble epoxide hydrolase and risk of ischemic stroke in a Chinese population. - Pharmacogenet Genomics - 2008 - Zhang L - Ding H - Yan J - Hui R - Wang W - Kissling GE - Zeldin DC - Wang DW - - - 10759591 - PubMed - Molecular mechanisms controlling nutritive blood flow: role of cytochrome P450 enzymes. - Acta Physiol Scand - 2000 - Harder DR - Roman RJ - Gebremedhin D - - - arachidonic acid metabolic pathway - PW:0000460 - Pathway Ontology - 14636671 PubMed @@ -438,33 +459,6 @@ Snyder GD Weintraub NL - - 15180494 - PubMed - Role of cytochrome P450 metabolites of arachidonic acid in hypertension. - Curr Drug Metab - 2004 - Sarkis A - Roman RJ - - - 3977905 - PubMed - On the metabolism of epoxyeicosatrienoic acids by ram seminal vesicles: isolation of 5(6)epoxy-prostaglandin F1 alpha. - Biochem Biophys Res Commun - 1985 - Oliw EH - Benthin G - - - 18383502 - PubMed - Gerry Brooks and epoxide hydrolases: four decades to a pharmaceutical. - Pest Manag Sci - 2008 - Morisseau C - Hammock BD - 17975109 PubMed @@ -481,35 +475,41 @@ Falck JR Miura H - - 4051502 + + 16399376 PubMed - Novel glutathione conjugates formed from epoxyeicosatrienoic acids (EETs). - Arch Biochem Biophys - 1985 - Spearman ME - Prough RA - Estabrook RW - Falck JR - Manna S - Leibman KC - Murphy RC - Capdevila J + Nomenclature for mammalian soluble glutathione transferases. + Methods Enzymol + 2005 + Mannervik B + Board PG + Hayes JD + Listowsky I + Pearson WR - - metabolic pathway of secondary metabolites - PW:0000147 - Pathway Ontology - - - 15748653 + + 18216721 PubMed - Epoxide hydrolases: their roles and interactions with lipid metabolism. - Prog Lipid Res - 2005 - Newman JW - Morisseau C - Hammock BD + Genetic variation in cytochrome P450 2J2 and soluble epoxide hydrolase and risk of ischemic stroke in a Chinese population. + Pharmacogenet Genomics + 2008 + Zhang L + Ding H + Yan J + Hui R + Wang W + Kissling GE + Zeldin DC + Wang DW + + + 15180494 + PubMed + Role of cytochrome P450 metabolites of arachidonic acid in hypertension. + Curr Drug Metab + 2004 + Sarkis A + Roman RJ diff --git a/pathways/WP1000/WP1000.json b/pathways/WP1000/WP1000.json index 772a1dab4..24425d162 100644 --- a/pathways/WP1000/WP1000.json +++ b/pathways/WP1000/WP1000.json @@ -2557,7 +2557,7 @@ "id": "publicationXrefb10", "source": "Pharmacogenet Genomics", "standardName": "Genetic variation in cytochrome P450 2J2 and soluble epoxide hydrolase and risk of ischemic stroke in a Chinese population.", - "textContent": "16", + "textContent": "18", "type": [ "PublicationXref", "PubMed:18216721" @@ -2599,7 +2599,7 @@ "id": "publicationXrefc2d", "source": "Circ Res", "standardName": "Hydrogen peroxide inhibits cytochrome p450 epoxygenases: interaction between two endothelium-derived hyperpolarizing factors.", - "textContent": "18", + "textContent": "17", "type": [ "PublicationXref", "PubMed:17975109" @@ -2663,7 +2663,7 @@ "id": "publicationXrefcdd", "source": "Arch Biochem Biophys", "standardName": "Novel glutathione conjugates formed from epoxyeicosatrienoic acids (EETs).", - "textContent": "3", + "textContent": "2", "type": [ "PublicationXref", "PubMed:4051502" @@ -2731,7 +2731,7 @@ "id": "publicationXrefdbf", "source": "Methods Enzymol", "standardName": "Nomenclature for mammalian soluble glutathione transferases.", - "textContent": "10", + "textContent": "12", "type": [ "PublicationXref", "PubMed:16399376" @@ -2768,7 +2768,7 @@ "id": "publicationXrefe2b", "source": "Biochem Biophys Res Commun", "standardName": "On the metabolism of epoxyeicosatrienoic acids by ram seminal vesicles: isolation of 5(6)epoxy-prostaglandin F1 alpha.", - "textContent": "2", + "textContent": "3", "type": [ "PublicationXref", "PubMed:3977905" @@ -2852,7 +2852,7 @@ "id": "publicationXreff0e", "source": "Pest Manag Sci", "standardName": "Gerry Brooks and epoxide hydrolases: four decades to a pharmaceutical.", - "textContent": "17", + "textContent": "16", "type": [ "PublicationXref", "PubMed:18383502" @@ -2909,7 +2909,7 @@ "id": "publicationXreff90", "source": "Prog Lipid Res", "standardName": "Epoxide hydrolases: their roles and interactions with lipid metabolism.", - "textContent": "12", + "textContent": "10", "type": [ "PublicationXref", "PubMed:15748653" diff --git a/pathways/WP1032/WP1032.gpml b/pathways/WP1032/WP1032.gpml index a88e64145..353902f05 100644 --- a/pathways/WP1032/WP1032.gpml +++ b/pathways/WP1032/WP1032.gpml @@ -635,22 +635,6 @@ - - NOD-like receptor signaling pathway - PW:0000817 - Pathway Ontology - - - 17110941 - PubMed - Nod-like proteins in immunity, inflammation and disease. - Nat Immunol - 2006 - Fritz JH - Ferrero RL - Philpott DJ - Girardin SE - 18161746 PubMed @@ -663,6 +647,15 @@ Philpott DJ Travassos LH + + 17186029 + PubMed + Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation. + Nat Rev Immunol + 2007 + Mariathasan S + Monack DM + 16823444 PubMed @@ -681,14 +674,16 @@ 2008 Kufer TA - - 17186029 + + 17110941 PubMed - Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation. - Nat Rev Immunol - 2007 - Mariathasan S - Monack DM + Nod-like proteins in immunity, inflammation and disease. + Nat Immunol + 2006 + Fritz JH + Ferrero RL + Philpott DJ + Girardin SE 18585455 @@ -701,6 +696,11 @@ Kim YG Nu�ez G + + NOD-like receptor signaling pathway + PW:0000817 + Pathway Ontology + diff --git a/pathways/WP1032/WP1032.json b/pathways/WP1032/WP1032.json index 146c7056b..d65a4390c 100644 --- a/pathways/WP1032/WP1032.json +++ b/pathways/WP1032/WP1032.json @@ -6334,7 +6334,7 @@ "id": "publicationXrefb56", "source": "Nat Immunol", "standardName": "Nod-like proteins in immunity, inflammation and disease.", - "textContent": "1", + "textContent": "2", "type": [ "PublicationXref", "PubMed:17110941" @@ -6408,7 +6408,7 @@ "id": "publicationXreff81", "source": "Nature", "standardName": "Intracellular pattern recognition receptors in the host response.", - "textContent": "2", + "textContent": "1", "type": [ "PublicationXref", "PubMed:16823444" diff --git a/pathways/WP1055/WP1055.gpml b/pathways/WP1055/WP1055.gpml index ba6d06048..e6006ca7e 100644 --- a/pathways/WP1055/WP1055.gpml +++ b/pathways/WP1055/WP1055.gpml @@ -1764,11 +1764,21 @@ Kandasamy, K., Mohan, S. S., Raju, R., Keerthikumar, S., Kumar, G. S. S., Venugo + + interleukin-4 signaling pathway + PW:0000912 + Pathway Ontology + Interleukin mediated signaling pathway PW:0000512 Pathway Ontology + + interleukin-4 signaling pathway + PW:0000912 + Pathway Ontology + 20067622 PubMed @@ -1816,21 +1826,11 @@ Kandasamy, K., Mohan, S. S., Raju, R., Keerthikumar, S., Kumar, G. S. S., Venugo Leonard WJ Pandey A - - interleukin-4 signaling pathway - PW:0000912 - Pathway Ontology - Interleukin mediated signaling pathway PW:0000512 Pathway Ontology - - interleukin-4 signaling pathway - PW:0000912 - Pathway Ontology - diff --git a/pathways/WP1055/WP1055.json b/pathways/WP1055/WP1055.json index 5c5fa7136..8fcb7e93a 100644 --- a/pathways/WP1055/WP1055.json +++ b/pathways/WP1055/WP1055.json @@ -14616,10 +14616,10 @@ "textContent": "Name: IL-4 signaling pathway\nLast Modified: 20240716182217\nOrganism: Bos taurus", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0000512", "http://identifiers.org/pw/PW:0000912", "http://identifiers.org/pw/PW:0000512", - "http://identifiers.org/pw/PW:0000912" + "http://identifiers.org/pw/PW:0000912", + "http://identifiers.org/pw/PW:0000512" ], "verticalAlign": "top", "width": 1156, diff --git a/pathways/WP1224/WP1224.gpml b/pathways/WP1224/WP1224.gpml index bb5164c5a..082d4effa 100644 --- a/pathways/WP1224/WP1224.gpml +++ b/pathways/WP1224/WP1224.gpml @@ -418,6 +418,11 @@ + + Epstein-Barr virus infection pathway + PW:0001057 + Pathway Ontology + 16477006 PubMed @@ -430,25 +435,20 @@ Kieff E Cahir-McFarland E - - 16446357 + + 18089854 PubMed - TAK1 is a component of the Epstein-Barr virus LMP1 complex and is essential for activation of JNK but not of NF-kappaB. - J Biol Chem - 2006 - Uemura N - Kajino T - Sanjo H - Sato S - Akira S - Matsumoto K - Ninomiya-Tsuji J + Hypoxia transcriptionally induces macrophage-inflammatory protein-3alpha/CCL-20 in primary human mononuclear phagocytes through nuclear factor (NF)-kappaB. + J Leukoc Biol + 2008 + Battaglia F + Delfino S + Merello E + Puppo M + Piva R + Varesio L + Bosco MC - - Epstein-Barr virus infection pathway - PW:0001057 - Pathway Ontology - 18052967 PubMed @@ -465,19 +465,19 @@ Paik TH Jo EK - - 18089854 + + 16446357 PubMed - Hypoxia transcriptionally induces macrophage-inflammatory protein-3alpha/CCL-20 in primary human mononuclear phagocytes through nuclear factor (NF)-kappaB. - J Leukoc Biol - 2008 - Battaglia F - Delfino S - Merello E - Puppo M - Piva R - Varesio L - Bosco MC + TAK1 is a component of the Epstein-Barr virus LMP1 complex and is essential for activation of JNK but not of NF-kappaB. + J Biol Chem + 2006 + Uemura N + Kajino T + Sanjo H + Sato S + Akira S + Matsumoto K + Ninomiya-Tsuji J diff --git a/pathways/WP1224/WP1224.json b/pathways/WP1224/WP1224.json index 7fd447a18..afbec0961 100644 --- a/pathways/WP1224/WP1224.json +++ b/pathways/WP1224/WP1224.json @@ -4023,7 +4023,7 @@ "id": "publicationXrefb42", "source": "J Leukoc Biol", "standardName": "Hypoxia transcriptionally induces macrophage-inflammatory protein-3alpha/CCL-20 in primary human mononuclear phagocytes through nuclear factor (NF)-kappaB.", - "textContent": "4", + "textContent": "3", "type": [ "PublicationXref", "PubMed:18089854" @@ -4092,7 +4092,7 @@ "id": "publicationXrefee4", "source": "Scand J Immunol", "standardName": "Expression and regulation of the CC-chemokine ligand 20 during human tuberculosis.", - "textContent": "3", + "textContent": "4", "type": [ "PublicationXref", "PubMed:18052967" diff --git a/pathways/WP1243/WP1243.gpml b/pathways/WP1243/WP1243.gpml index d005e0f3a..a9efe4f36 100644 --- a/pathways/WP1243/WP1243.gpml +++ b/pathways/WP1243/WP1243.gpml @@ -466,20 +466,6 @@ PW:0001057 Pathway Ontology - - 16446357 - PubMed - TAK1 is a component of the Epstein-Barr virus LMP1 complex and is essential for activation of JNK but not of NF-kappaB. - J Biol Chem - 2006 - Uemura N - Kajino T - Sanjo H - Sato S - Akira S - Matsumoto K - Ninomiya-Tsuji J - 18089854 PubMed @@ -494,6 +480,20 @@ Varesio L Bosco MC + + 16446357 + PubMed + TAK1 is a component of the Epstein-Barr virus LMP1 complex and is essential for activation of JNK but not of NF-kappaB. + J Biol Chem + 2006 + Uemura N + Kajino T + Sanjo H + Sato S + Akira S + Matsumoto K + Ninomiya-Tsuji J + diff --git a/pathways/WP1250/WP1250.gpml b/pathways/WP1250/WP1250.gpml index 180e86ef2..6ec42188a 100644 --- a/pathways/WP1250/WP1250.gpml +++ b/pathways/WP1250/WP1250.gpml @@ -283,29 +283,6 @@ - - 2834948 - PubMed - Novel renal arachidonate metabolites. - Am J Med Sci - 1988 - Carroll MA - Schwartzman M - Sacerdoti D - McGiff JC - - - 16399376 - PubMed - Nomenclature for mammalian soluble glutathione transferases. - Methods Enzymol - 2005 - Mannervik B - Board PG - Hayes JD - Listowsky I - Pearson WR - 16258029 PubMed @@ -321,14 +298,50 @@ Falck JR Gutterman DD - - 3977905 + + arachidonic acid metabolic pathway + PW:0000460 + Pathway Ontology + + + 15748653 PubMed - On the metabolism of epoxyeicosatrienoic acids by ram seminal vesicles: isolation of 5(6)epoxy-prostaglandin F1 alpha. - Biochem Biophys Res Commun + Epoxide hydrolases: their roles and interactions with lipid metabolism. + Prog Lipid Res + 2005 + Newman JW + Morisseau C + Hammock BD + + + 18216721 + PubMed + Genetic variation in cytochrome P450 2J2 and soluble epoxide hydrolase and risk of ischemic stroke in a Chinese population. + Pharmacogenet Genomics + 2008 + Zhang L + Ding H + Yan J + Hui R + Wang W + Kissling GE + Zeldin DC + Wang DW + + + 4051502 + PubMed + Novel glutathione conjugates formed from epoxyeicosatrienoic acids (EETs). + Arch Biochem Biophys 1985 - Oliw EH - Benthin G + Spearman ME + Prough RA + Estabrook RW + Falck JR + Manna S + Leibman KC + Murphy RC + Capdevila J 17494091 @@ -342,30 +355,24 @@ Zeldin DC Wegmann M - - 17164131 + + 3977905 PubMed - Soluble epoxide hydrolase inhibition reveals novel biological functions of epoxyeicosatrienoic acids (EETs). - Prostaglandins Other Lipid Mediat - 2007 - Inceoglu B - Schmelzer KR - Morisseau C - Jinks SL - Hammock BD + On the metabolism of epoxyeicosatrienoic acids by ram seminal vesicles: isolation of 5(6)epoxy-prostaglandin F1 alpha. + Biochem Biophys Res Commun + 1985 + Oliw EH + Benthin G - - arachidonic acid metabolic pathway - PW:0000460 - Pathway Ontology - - - 6548162 + + 14626496 PubMed - Biosynthesis of 5,6-dihydroxyprostaglandin E1 and F1 alpha from 5,6-dihydroxyeicosatrienoic acid by ram seminal vesicles. - Biochim Biophys Acta - 1984 - Oliw EH + Role of cytochrome P450-dependent arachidonic acid metabolites in liver physiology and pathophysiology. + Prostaglandins Other Lipid Mediat + 2003 + Sacerdoti D + Gatta A + McGiff JC 16179585 @@ -385,46 +392,37 @@ Busse R Nilius B - - 14626496 + + 14636671 PubMed - Role of cytochrome P450-dependent arachidonic acid metabolites in liver physiology and pathophysiology. - Prostaglandins Other Lipid Mediat - 2003 - Sacerdoti D - Gatta A - McGiff JC + Epoxyeicosatrienoic acids (EETs): metabolism and biochemical function. + Prog Lipid Res + 2004 + Spector AA + Fang X + Snyder GD + Weintraub NL - - 17975109 + + 2834948 PubMed - Hydrogen peroxide inhibits cytochrome p450 epoxygenases: interaction between two endothelium-derived hyperpolarizing factors. - Circ Res - 2008 - Larsen BT - Gutterman DD - Sato A - Toyama K - Campbell WB - Zeldin DC - Manthati VL - Falck JR - Miura H + Novel renal arachidonate metabolites. + Am J Med Sci + 1988 + Carroll MA + Schwartzman M + Sacerdoti D + McGiff JC - - 18216721 + + 10759591 PubMed - Genetic variation in cytochrome P450 2J2 and soluble epoxide hydrolase and risk of ischemic stroke in a Chinese population. - Pharmacogenet Genomics - 2008 - Zhang L - Ding H - Yan J - Hui R - Wang W - Kissling GE - Zeldin DC - Wang DW + Molecular mechanisms controlling nutritive blood flow: role of cytochrome P450 enzymes. + Acta Physiol Scand + 2000 + Harder DR + Roman RJ + Gebremedhin D 18383502 @@ -435,25 +433,62 @@ Morisseau C Hammock BD - - 15748653 + + 16399376 PubMed - Epoxide hydrolases: their roles and interactions with lipid metabolism. - Prog Lipid Res + Nomenclature for mammalian soluble glutathione transferases. + Methods Enzymol 2005 - Newman JW + Mannervik B + Board PG + Hayes JD + Listowsky I + Pearson WR + + + 6548162 + PubMed + Biosynthesis of 5,6-dihydroxyprostaglandin E1 and F1 alpha from 5,6-dihydroxyeicosatrienoic acid by ram seminal vesicles. + Biochim Biophys Acta + 1984 + Oliw EH + + + 15180494 + PubMed + Role of cytochrome P450 metabolites of arachidonic acid in hypertension. + Curr Drug Metab + 2004 + Sarkis A + Roman RJ + + + 17164131 + PubMed + Soluble epoxide hydrolase inhibition reveals novel biological functions of epoxyeicosatrienoic acids (EETs). + Prostaglandins Other Lipid Mediat + 2007 + Inceoglu B + Schmelzer KR Morisseau C + Jinks SL Hammock BD - - 10759591 + + 17975109 PubMed - Molecular mechanisms controlling nutritive blood flow: role of cytochrome P450 enzymes. - Acta Physiol Scand - 2000 - Harder DR - Roman RJ - Gebremedhin D + Hydrogen peroxide inhibits cytochrome p450 epoxygenases: interaction between two endothelium-derived hyperpolarizing factors. + Circ Res + 2008 + Larsen BT + Gutterman DD + Sato A + Toyama K + Campbell WB + Zeldin DC + Manthati VL + Falck JR + Miura H 3619897 @@ -467,41 +502,6 @@ Blair IA Falck JR - - 4051502 - PubMed - Novel glutathione conjugates formed from epoxyeicosatrienoic acids (EETs). - Arch Biochem Biophys - 1985 - Spearman ME - Prough RA - Estabrook RW - Falck JR - Manna S - Leibman KC - Murphy RC - Capdevila J - - - 15180494 - PubMed - Role of cytochrome P450 metabolites of arachidonic acid in hypertension. - Curr Drug Metab - 2004 - Sarkis A - Roman RJ - - - 14636671 - PubMed - Epoxyeicosatrienoic acids (EETs): metabolism and biochemical function. - Prog Lipid Res - 2004 - Spector AA - Fang X - Snyder GD - Weintraub NL - diff --git a/pathways/WP1250/WP1250.json b/pathways/WP1250/WP1250.json index d9eebb3b2..e3ae11da5 100644 --- a/pathways/WP1250/WP1250.json +++ b/pathways/WP1250/WP1250.json @@ -2464,7 +2464,7 @@ "id": "publicationXrefb10", "source": "Pharmacogenet Genomics", "standardName": "Genetic variation in cytochrome P450 2J2 and soluble epoxide hydrolase and risk of ischemic stroke in a Chinese population.", - "textContent": "17", + "textContent": "16", "type": [ "PublicationXref", "PubMed:18216721" @@ -2506,7 +2506,7 @@ "id": "publicationXrefc2d", "source": "Circ Res", "standardName": "Hydrogen peroxide inhibits cytochrome p450 epoxygenases: interaction between two endothelium-derived hyperpolarizing factors.", - "textContent": "16", + "textContent": "18", "type": [ "PublicationXref", "PubMed:17975109" @@ -2570,7 +2570,7 @@ "id": "publicationXrefcdd", "source": "Arch Biochem Biophys", "standardName": "Novel glutathione conjugates formed from epoxyeicosatrienoic acids (EETs).", - "textContent": "3", + "textContent": "2", "type": [ "PublicationXref", "PubMed:4051502" @@ -2617,7 +2617,7 @@ "id": "publicationXrefd99", "source": "Prog Lipid Res", "standardName": "Epoxyeicosatrienoic acids (EETs): metabolism and biochemical function.", - "textContent": "9", + "textContent": "8", "type": [ "PublicationXref", "PubMed:14636671" @@ -2638,7 +2638,7 @@ "id": "publicationXrefdbf", "source": "Methods Enzymol", "standardName": "Nomenclature for mammalian soluble glutathione transferases.", - "textContent": "10", + "textContent": "12", "type": [ "PublicationXref", "PubMed:16399376" @@ -2675,7 +2675,7 @@ "id": "publicationXrefe2b", "source": "Biochem Biophys Res Commun", "standardName": "On the metabolism of epoxyeicosatrienoic acids by ram seminal vesicles: isolation of 5(6)epoxy-prostaglandin F1 alpha.", - "textContent": "2", + "textContent": "3", "type": [ "PublicationXref", "PubMed:3977905" @@ -2759,7 +2759,7 @@ "id": "publicationXreff0e", "source": "Pest Manag Sci", "standardName": "Gerry Brooks and epoxide hydrolases: four decades to a pharmaceutical.", - "textContent": "18", + "textContent": "17", "type": [ "PublicationXref", "PubMed:18383502" @@ -2797,7 +2797,7 @@ "id": "publicationXreff4f", "source": "Curr Drug Metab", "standardName": "Role of cytochrome P450 metabolites of arachidonic acid in hypertension.", - "textContent": "8", + "textContent": "9", "type": [ "PublicationXref", "PubMed:15180494" @@ -2816,7 +2816,7 @@ "id": "publicationXreff90", "source": "Prog Lipid Res", "standardName": "Epoxide hydrolases: their roles and interactions with lipid metabolism.", - "textContent": "12", + "textContent": "10", "type": [ "PublicationXref", "PubMed:15748653" diff --git a/pathways/WP1256/WP1256.gpml b/pathways/WP1256/WP1256.gpml index 38a8435c1..23db2221b 100644 --- a/pathways/WP1256/WP1256.gpml +++ b/pathways/WP1256/WP1256.gpml @@ -635,6 +635,10 @@ + + PubMed + kufer t + 18414735 PubMed @@ -643,25 +647,6 @@ 2008 Kufer TA - - 16823444 - PubMed - Intracellular pattern recognition receptors in the host response. - Nature - 2006 - Meylan E - Tschopp J - Karin M - - - NOD-like receptor signaling pathway - PW:0000817 - Pathway Ontology - - - PubMed - kufer t - 18161746 PubMed @@ -674,6 +659,16 @@ Philpott DJ Travassos LH + + 16823444 + PubMed + Intracellular pattern recognition receptors in the host response. + Nature + 2006 + Meylan E + Tschopp J + Karin M + 17110941 PubMed @@ -685,6 +680,11 @@ Philpott DJ Girardin SE + + NOD-like receptor signaling pathway + PW:0000817 + Pathway Ontology + 18585455 PubMed diff --git a/pathways/WP1256/WP1256.json b/pathways/WP1256/WP1256.json index 67ceb49b7..e69615a29 100644 --- a/pathways/WP1256/WP1256.json +++ b/pathways/WP1256/WP1256.json @@ -6305,7 +6305,7 @@ ], "gpmlElementName": "PublicationXref", "id": "publicationXrefb3c", - "textContent": "3", + "textContent": "1", "type": [ "PublicationXref" ], @@ -6322,7 +6322,7 @@ "id": "publicationXrefb56", "source": "Nat Immunol", "standardName": "Nod-like proteins in immunity, inflammation and disease.", - "textContent": "4", + "textContent": "3", "type": [ "PublicationXref", "PubMed:17110941" @@ -6340,7 +6340,7 @@ "id": "publicationXrefc28", "source": "Nat Rev Immunol", "standardName": "Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation.", - "textContent": "5", + "textContent": "4", "type": [ "PublicationXref", "PubMed:17186029" @@ -6357,7 +6357,7 @@ "id": "publicationXrefd56", "source": "Mol Biosyst", "standardName": "Signal transduction pathways used by NLR-type innate immune receptors.", - "textContent": "2", + "textContent": "5", "type": [ "PublicationXref", "PubMed:18414735" @@ -6396,7 +6396,7 @@ "id": "publicationXreff81", "source": "Nature", "standardName": "Intracellular pattern recognition receptors in the host response.", - "textContent": "1", + "textContent": "2", "type": [ "PublicationXref", "PubMed:16823444" diff --git a/pathways/WP1273/WP1273.gpml b/pathways/WP1273/WP1273.gpml index 55c7f6367..c26562f33 100644 --- a/pathways/WP1273/WP1273.gpml +++ b/pathways/WP1273/WP1273.gpml @@ -2603,56 +2603,63 @@ - - 8846925 + + 8968737 PubMed - Free radicals, uric acid, and human disease. - Free Radic Biol Med. + Human methionine synthase: cDNA cloning and identification of mutations in patients of the cblG complementation group of folate/cobalamin disorders. + Hum Mol Genet. 1996 - Proctor PH. + Leclerc D + Campeau E + Goyette P + Adjalla CE + Christensen B + Ross M + Eydoux P + Rosenblatt DS + Rozen R + Gravel RA. - - 840498 + + 6295699 PubMed - Cystathionine beta-synthase deficiency: a qualitative abnormality of the deficient enzyme modified by vitamin B6 therapy. - Pediatr Res. - 1977 - Longhi RC - Fleisher LD - Tallan HH - Gaull GE. + Vitamin B12 binders (transcobalamins) in serum. + Crit Rev Clin Lab Sci. + 1982 + Fernandes-Costa F: Metz J. - - WP28 - WikiPathways - Selenoproteins - http://www.wikipathways.org/index.php/Pathway:Homo_sapiens:Selenoproteins - WikiPathways + + pathway of folate cycle/metabolism + PW:0000140 + Pathway Ontology + + + 10448523 + PubMed + Homocysteine metabolism. + Annu Rev Nutr + 1999 + Selhub J. - + - Prostaglandin and Leukotriene Metabolism - Ingenuity software - https://analysis.ingenuity.com/pa/ + Folic acid + Linus Pauling Institute + http://lpi.oregonstate.edu/infocenter/vitamins/fa/ - - 16962588 + + 11731805 PubMed - Identification and characterization of selenoprotein K: an antioxidant in cardiomyocytes. - FEBS Lett. - 2006 - Lu C - Qiu F - Zhou H - Peng Yp - Hao W - Xu J - Yuan J - Wang S - Qiang B - Xu C - Peng X. + Domain alternation switches B(12)-dependent methionine synthase to the activation conformation. + Nat Struct Biol. + 2002 + Bandarian V + Pattridge KA + Lennon BW + Huddler DP + Matthews RG + Ludwig ML. 6300970 @@ -2670,26 +2677,6 @@ Larue M Rokach J. - - 10.1021/bi981808n - DOI - Binding of Pyridoxal 5'-Phosphate to the Heme Protein Human Cystathionine β-Synthase - Biochemistry 38(9) - 1999 - Vladimir Kery - Loelle Poneleit - Jeffrey D. Meyer - Mark C. Manning - Jan P. Kraus - - - 1184739 - PubMed - Transcobalamins I and II as natural transport proteins of vitamin B12. - The Journal of clinical investigation - 1975 - Hall CA - 18466421 PubMed @@ -2699,35 +2686,47 @@ George J Struthers AD. - - 6295699 + + 840498 PubMed - Vitamin B12 binders (transcobalamins) in serum. - Crit Rev Clin Lab Sci. - 1982 - Fernandes-Costa F: Metz J. - - - - - Folic acid - Linus Pauling Institute - http://lpi.oregonstate.edu/infocenter/vitamins/fa/ + Cystathionine beta-synthase deficiency: a qualitative abnormality of the deficient enzyme modified by vitamin B6 therapy. + Pediatr Res. + 1977 + Longhi RC + Fleisher LD + Tallan HH + Gaull GE. - - 10448523 + + 14726604 PubMed - Homocysteine metabolism. - Annu Rev Nutr + Nitric oxide and superoxide in inflammation and immune regulation. + J Physiol Pharmacol. + 2003 + Guzik TJ + Korbut R + Adamek-Guzik T. + + + 10.1021/bi981808n + DOI + Binding of Pyridoxal 5'-Phosphate to the Heme Protein Human Cystathionine β-Synthase + Biochemistry 38(9) 1999 - Selhub J. + Vladimir Kery + Loelle Poneleit + Jeffrey D. Meyer + Mark C. Manning + Jan P. Kraus - - - - Prostaglandin and Leukotriene Metabolism - Ingenuity software - https://analysis.ingenuity.com/ + + 8534261 + PubMed + The isoprostanes. Current knowledge and directions for future research. + Biochem Pharmacol. + 1996 + Morrow JD + Roberts LJ 2nd. 18598592 @@ -2742,53 +2741,20 @@ Augustin Scalbert Suzan Wopereis - - 8534261 - PubMed - The isoprostanes. Current knowledge and directions for future research. - Biochem Pharmacol. - 1996 - Morrow JD - Roberts LJ 2nd. - - - 10448523 - PubMed - Homocysteine metabolism. - Annu Rev Nutr. - 1999 - Selhub J. - - + - Arachidonic Acid Metabolism - Ingenuity sofware + Prostaglandin and Leukotriene Metabolism + Ingenuity software https://analysis.ingenuity.com/ - - 15104204 - PubMed - Isoprostanes: novel bioactive products of lipid peroxidation. - Free Radic Res. - 2004 - Basu S. - - - 16011463 - PubMed - Vitamin E, oxidative stress, and inflammation. - Annu Rev Nutr. - 2005 - Singh U - Devaraj S - Jialal I. + + + + Prostaglandin and Leukotriene Metabolism + Ingenuity software + https://analysis.ingenuity.com/pa/ - - pathway of folate cycle/metabolism - PW:0000140 - Pathway Ontology - 18409172 PubMed @@ -2800,40 +2766,20 @@ Smith EJ Hagen TM. - - 16047261 - PubMed - Homocysteine: overview of biochemistry, molecular biology, and role in disease processes. - Semin Vasc Med - 2005 - Fowler B. - - - 8968737 - PubMed - Human methionine synthase: cDNA cloning and identification of mutations in patients of the cblG complementation group of folate/cobalamin disorders. - Hum Mol Genet. - 1996 - Leclerc D - Campeau E - Goyette P - Adjalla CE - Christensen B - Ross M - Eydoux P - Rosenblatt DS - Rozen R - Gravel RA. + + + + Vitamin B 6 + Linus Paulin institute + http://lpi.oregonstate.edu/infocenter/vitamins/vitaminB6/ - - 14726604 + + 1184739 PubMed - Nitric oxide and superoxide in inflammation and immune regulation. - J Physiol Pharmacol. - 2003 - Guzik TJ - Korbut R - Adamek-Guzik T. + Transcobalamins I and II as natural transport proteins of vitamin B12. + The Journal of clinical investigation + 1975 + Hall CA 11929995 @@ -2847,6 +2793,22 @@ Sun Z Gladyshev VN. + + 10448523 + PubMed + Homocysteine metabolism. + Annu Rev Nutr. + 1999 + Selhub J. + + + 15104204 + PubMed + Isoprostanes: novel bioactive products of lipid peroxidation. + Free Radic Res. + 2004 + Basu S. + 10444342 PubMed @@ -2855,25 +2817,13 @@ 1999 Wilson A, Platt R, Wu Q, Leclerc D, Christensen B, Yang H, Gravel RA, Rozen R - - - - Vitamin B 6 - Linus Paulin institute - http://lpi.oregonstate.edu/infocenter/vitamins/vitaminB6/ - - - 11731805 + + 16047261 PubMed - Domain alternation switches B(12)-dependent methionine synthase to the activation conformation. - Nat Struct Biol. - 2002 - Bandarian V - Pattridge KA - Lennon BW - Huddler DP - Matthews RG - Ludwig ML. + Homocysteine: overview of biochemistry, molecular biology, and role in disease processes. + Semin Vasc Med + 2005 + Fowler B. 978-0-309-06411-8 @@ -2882,6 +2832,56 @@ Washington D.C.: National Academies Press 1998 + + 8846925 + PubMed + Free radicals, uric acid, and human disease. + Free Radic Biol Med. + 1996 + Proctor PH. + + + + + Arachidonic Acid Metabolism + Ingenuity sofware + https://analysis.ingenuity.com/ + + + 16962588 + PubMed + Identification and characterization of selenoprotein K: an antioxidant in cardiomyocytes. + FEBS Lett. + 2006 + Lu C + Qiu F + Zhou H + Peng Yp + Hao W + Xu J + Yuan J + Wang S + Qiang B + Xu C + Peng X. + + + WP28 + WikiPathways + Selenoproteins + http://www.wikipathways.org/index.php/Pathway:Homo_sapiens:Selenoproteins + WikiPathways + + + 16011463 + PubMed + Vitamin E, oxidative stress, and inflammation. + Annu Rev Nutr. + 2005 + Singh U + Devaraj S + Jialal I. + diff --git a/pathways/WP1273/WP1273.json b/pathways/WP1273/WP1273.json index 3d8e9ea0f..c4daea646 100644 --- a/pathways/WP1273/WP1273.json +++ b/pathways/WP1273/WP1273.json @@ -23228,7 +23228,7 @@ "id": "publicationXrefa21", "source": "FEBS Lett.", "standardName": "Identification and characterization of selenoprotein K: an antioxidant in cardiomyocytes.", - "textContent": "16", + "textContent": "23", "type": [ "PublicationXref", "PubMed:16962588" @@ -23269,7 +23269,7 @@ "id": "publicationXrefa58", "source": "IUBMB Life.", "standardName": "Is alpha-lipoic acid a scavenger of reactive oxygen species in vivo? Evidence for its initiation of stress signaling pathways that promote endogenous antioxidant capacity.", - "textContent": "27", + "textContent": "24", "type": [ "PublicationXref", "PubMed:18409172" @@ -23287,7 +23287,7 @@ "id": "publicationXrefa62", "source": "Biochem Pharmacol.", "standardName": "The isoprostanes. Current knowledge and directions for future research.", - "textContent": "8", + "textContent": "10", "type": [ "PublicationXref", "PubMed:8534261" @@ -23304,7 +23304,7 @@ "id": "publicationXrefa89", "source": "Ingenuity software", "standardName": "Prostaglandin and Leukotriene Metabolism", - "textContent": "4", + "textContent": "19", "type": [ "PublicationXref" ] @@ -23317,7 +23317,7 @@ "id": "publicationXrefb83", "source": "Linus Pauling Institute", "standardName": "Folic acid", - "textContent": "18", + "textContent": "9", "type": [ "PublicationXref" ] @@ -23327,7 +23327,7 @@ "id": "publicationXrefb89", "source": "Washington D.C.: National Academies Press", "standardName": "Food and Nutrition Board, Institute of Medicine. Vitamin B6. Dietary Reference Intakes: Thiamin, Riboflavin, Niacin, Vitamin B6, Vitamin B12, Pantothenic Acid, Biotin, and Choline.", - "textContent": "10", + "textContent": "7", "type": [ "PublicationXref", "ISBN:978-0-309-06411-8" @@ -23352,7 +23352,7 @@ "id": "publicationXrefbbd", "source": "Prostaglandins.", "standardName": "Synthesis and biological activities of leukotriene F4 and leukotriene F4 sulfone", - "textContent": "6", + "textContent": "4", "type": [ "PublicationXref", "PubMed:6300970" @@ -23372,7 +23372,7 @@ "id": "publicationXrefbc2", "source": "Pediatr Res.", "standardName": "Cystathionine beta-synthase deficiency: a qualitative abnormality of the deficient enzyme modified by vitamin B6 therapy.", - "textContent": "1", + "textContent": "2", "type": [ "PublicationXref", "PubMed:840498" @@ -23394,7 +23394,7 @@ "id": "publicationXrefc1b", "source": "Br J Nutr", "standardName": "A network biology model of micronutrient related health", - "textContent": "24", + "textContent": "17", "type": [ "PublicationXref", "PubMed:18598592" @@ -23432,7 +23432,7 @@ "id": "publicationXrefca8", "source": "Molecular genetics and metabolism", "standardName": "A common variant in methionine synthase reductase combined with low cobalamin (vitamin B12) increases risk for spina bifida.", - "textContent": "14", + "textContent": "13", "type": [ "PublicationXref", "PubMed:10444342" @@ -23454,7 +23454,7 @@ "id": "publicationXrefcbd", "source": "Nat Struct Biol.", "standardName": "Domain alternation switches B(12)-dependent methionine synthase to the activation conformation.", - "textContent": "15", + "textContent": "14", "type": [ "PublicationXref", "PubMed:11731805" @@ -23480,7 +23480,7 @@ "id": "publicationXrefcc4", "source": "Hum Mol Genet.", "standardName": "Human methionine synthase: cDNA cloning and identification of mutations in patients of the cblG complementation group of folate/cobalamin disorders.", - "textContent": "9", + "textContent": "5", "type": [ "PublicationXref", "PubMed:8968737" @@ -23497,7 +23497,7 @@ "id": "publicationXrefcd4", "source": "Semin Vasc Med", "standardName": "Homocysteine: overview of biochemistry, molecular biology, and role in disease processes.", - "textContent": "26", + "textContent": "22", "type": [ "PublicationXref", "PubMed:16047261" @@ -23514,7 +23514,7 @@ "id": "publicationXrefce8", "source": "Free Radic Res.", "standardName": "Isoprostanes: novel bioactive products of lipid peroxidation.", - "textContent": "22", + "textContent": "21", "type": [ "PublicationXref", "PubMed:15104204" @@ -23531,7 +23531,7 @@ "id": "publicationXrefcf3", "source": "Annu Rev Nutr", "standardName": "Homocysteine metabolism.", - "textContent": "12", + "textContent": "8", "type": [ "PublicationXref", "PubMed:10448523" @@ -23548,7 +23548,7 @@ "id": "publicationXrefdab", "source": "Crit Rev Clin Lab Sci.", "standardName": "Vitamin B12 binders (transcobalamins) in serum.", - "textContent": "7", + "textContent": "3", "type": [ "PublicationXref", "PubMed:6295699" @@ -23567,7 +23567,7 @@ "id": "publicationXrefdc8", "source": "Annu Rev Nutr.", "standardName": "Vitamin E, oxidative stress, and inflammation.", - "textContent": "23", + "textContent": "28", "type": [ "PublicationXref", "PubMed:16011463" @@ -23584,7 +23584,7 @@ "id": "publicationXrefe10", "source": "The Journal of clinical investigation", "standardName": "Transcobalamins I and II as natural transport proteins of vitamin B12.", - "textContent": "5", + "textContent": "1", "type": [ "PublicationXref", "PubMed:1184739" @@ -23601,7 +23601,7 @@ "id": "publicationXrefe80", "source": "Linus Paulin institute", "standardName": "Vitamin B 6", - "textContent": "28", + "textContent": "25", "type": [ "PublicationXref" ] @@ -23616,7 +23616,7 @@ "id": "publicationXrefebb", "source": "J Physiol Pharmacol.", "standardName": "Nitric oxide and superoxide in inflammation and immune regulation.", - "textContent": "21", + "textContent": "15", "type": [ "PublicationXref", "PubMed:14726604" @@ -23633,7 +23633,7 @@ "id": "publicationXrefec3", "source": "http://www.wikipathways.org/index.php/Pathway:Homo_sapiens:Selenoproteins", "standardName": "Selenoproteins", - "textContent": "3", + "textContent": "27", "type": [ "PublicationXref", "WikiPathways:WP28" @@ -23650,7 +23650,7 @@ "id": "publicationXrefed9", "source": "Cardiovasc Ther.", "standardName": "The role of urate and xanthine oxidase inhibitors in cardiovascular disease.", - "textContent": "17", + "textContent": "16", "type": [ "PublicationXref", "PubMed:18466421" @@ -23667,7 +23667,7 @@ "id": "publicationXreff15", "source": "Free Radic Biol Med.", "standardName": "Free radicals, uric acid, and human disease.", - "textContent": "2", + "textContent": "6", "type": [ "PublicationXref", "PubMed:8846925" @@ -23684,7 +23684,7 @@ "id": "publicationXreff1b", "source": "Annu Rev Nutr.", "standardName": "Homocysteine metabolism.", - "textContent": "13", + "textContent": "12", "type": [ "PublicationXref", "PubMed:10448523" @@ -23701,7 +23701,7 @@ "id": "publicationXreff96", "source": "Ingenuity software", "standardName": "Prostaglandin and Leukotriene Metabolism", - "textContent": "19", + "textContent": "18", "type": [ "PublicationXref" ] @@ -23714,7 +23714,7 @@ "id": "publicationXrefff2", "source": "Ingenuity sofware", "standardName": "Arachidonic Acid Metabolism", - "textContent": "25", + "textContent": "26", "type": [ "PublicationXref" ] diff --git a/pathways/WP1278/WP1278.gpml b/pathways/WP1278/WP1278.gpml index 359ef5866..a0d43c23c 100644 --- a/pathways/WP1278/WP1278.gpml +++ b/pathways/WP1278/WP1278.gpml @@ -449,27 +449,25 @@ Matsumoto K Ninomiya-Tsuji J - - 18052967 - PubMed - Expression and regulation of the CC-chemokine ligand 20 during human tuberculosis. - Scand J Immunol - 2008 - Lee JS - Lee JY - Son JW - Oh JH - Shin DM - Yuk JM - Song CH - Paik TH - Jo EK - Epstein-Barr virus infection pathway PW:0001057 Pathway Ontology + + 18089854 + PubMed + Hypoxia transcriptionally induces macrophage-inflammatory protein-3alpha/CCL-20 in primary human mononuclear phagocytes through nuclear factor (NF)-kappaB. + J Leukoc Biol + 2008 + Battaglia F + Delfino S + Merello E + Puppo M + Piva R + Varesio L + Bosco MC + 16477006 PubMed @@ -482,19 +480,21 @@ Kieff E Cahir-McFarland E - - 18089854 + + 18052967 PubMed - Hypoxia transcriptionally induces macrophage-inflammatory protein-3alpha/CCL-20 in primary human mononuclear phagocytes through nuclear factor (NF)-kappaB. - J Leukoc Biol + Expression and regulation of the CC-chemokine ligand 20 during human tuberculosis. + Scand J Immunol 2008 - Battaglia F - Delfino S - Merello E - Puppo M - Piva R - Varesio L - Bosco MC + Lee JS + Lee JY + Son JW + Oh JH + Shin DM + Yuk JM + Song CH + Paik TH + Jo EK diff --git a/pathways/WP1278/WP1278.json b/pathways/WP1278/WP1278.json index df12392dd..c545e7302 100644 --- a/pathways/WP1278/WP1278.json +++ b/pathways/WP1278/WP1278.json @@ -3911,7 +3911,7 @@ "id": "publicationXrefb42", "source": "J Leukoc Biol", "standardName": "Hypoxia transcriptionally induces macrophage-inflammatory protein-3alpha/CCL-20 in primary human mononuclear phagocytes through nuclear factor (NF)-kappaB.", - "textContent": "4", + "textContent": "3", "type": [ "PublicationXref", "PubMed:18089854" @@ -3980,7 +3980,7 @@ "id": "publicationXrefee4", "source": "Scand J Immunol", "standardName": "Expression and regulation of the CC-chemokine ligand 20 during human tuberculosis.", - "textContent": "3", + "textContent": "4", "type": [ "PublicationXref", "PubMed:18052967" diff --git a/pathways/WP1294/WP1294.gpml b/pathways/WP1294/WP1294.gpml index cf133661e..507008872 100644 --- a/pathways/WP1294/WP1294.gpml +++ b/pathways/WP1294/WP1294.gpml @@ -635,18 +635,6 @@ - - 18161746 - PubMed - Nod-like proteins in inflammation and disease. - J Pathol - 2008 - Carneiro LA - Magalhaes JG - Tattoli I - Philpott DJ - Travassos LH - 16823444 PubMed @@ -657,19 +645,16 @@ Tschopp J Karin M - - NOD-like receptor signaling pathway - PW:0000817 - Pathway Ontology - - - 17186029 + + 18585455 PubMed - Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation. - Nat Rev Immunol - 2007 - Mariathasan S - Monack DM + NOD-like receptors (NLRs): bona fide intracellular microbial sensors. + Curr Opin Immunol + 2008 + Shaw MH + Reimer T + Kim YG + Nu�ez G 17110941 @@ -682,6 +667,32 @@ Philpott DJ Girardin SE + + 18161746 + PubMed + Nod-like proteins in inflammation and disease. + J Pathol + 2008 + Carneiro LA + Magalhaes JG + Tattoli I + Philpott DJ + Travassos LH + + + 17186029 + PubMed + Inflammasome adaptors and sensors: intracellular regulators of infection and inflammation. + Nat Rev Immunol + 2007 + Mariathasan S + Monack DM + + + NOD-like receptor signaling pathway + PW:0000817 + Pathway Ontology + 18414735 PubMed @@ -690,17 +701,6 @@ 2008 Kufer TA - - 18585455 - PubMed - NOD-like receptors (NLRs): bona fide intracellular microbial sensors. - Curr Opin Immunol - 2008 - Shaw MH - Reimer T - Kim YG - Nu�ez G - diff --git a/pathways/WP1294/WP1294.json b/pathways/WP1294/WP1294.json index 6461dbd9e..cbf168386 100644 --- a/pathways/WP1294/WP1294.json +++ b/pathways/WP1294/WP1294.json @@ -6254,7 +6254,7 @@ "id": "publicationXrefb26", "source": "J Pathol", "standardName": "Nod-like proteins in inflammation and disease.", - "textContent": "4", + "textContent": "5", "type": [ "PublicationXref", "PubMed:18161746" @@ -6309,7 +6309,7 @@ "id": "publicationXrefd56", "source": "Mol Biosyst", "standardName": "Signal transduction pathways used by NLR-type innate immune receptors.", - "textContent": "5", + "textContent": "6", "type": [ "PublicationXref", "PubMed:18414735" @@ -6329,7 +6329,7 @@ "id": "publicationXreff78", "source": "Curr Opin Immunol", "standardName": "NOD-like receptors (NLRs): bona fide intracellular microbial sensors.", - "textContent": "6", + "textContent": "4", "type": [ "PublicationXref", "PubMed:18585455" diff --git a/pathways/WP1311/WP1311.gpml b/pathways/WP1311/WP1311.gpml index 3cd1ec5ac..bf306f478 100644 --- a/pathways/WP1311/WP1311.gpml +++ b/pathways/WP1311/WP1311.gpml @@ -2615,13 +2615,21 @@ - - 10448523 + + 978-0-309-06411-8 + ISBN + Food and Nutrition Board, Institute of Medicine. Vitamin B6. Dietary Reference Intakes: Thiamin, Riboflavin, Niacin, Vitamin B6, Vitamin B12, Pantothenic Acid, Biotin, and Choline. + Washington D.C.: National Academies Press + 1998 + + + 8534261 PubMed - Homocysteine metabolism. - Annu Rev Nutr. - 1999 - Selhub J. + The isoprostanes. Current knowledge and directions for future research. + Biochem Pharmacol. + 1996 + Morrow JD + Roberts LJ 2nd. 11929995 @@ -2635,19 +2643,41 @@ Sun Z Gladyshev VN. - - - - Vitamin B 6 - Linus Paulin institute - http://lpi.oregonstate.edu/infocenter/vitamins/vitaminB6/ + + 18409172 + PubMed + Is alpha-lipoic acid a scavenger of reactive oxygen species in vivo? Evidence for its initiation of stress signaling pathways that promote endogenous antioxidant capacity. + IUBMB Life. + 2008 + Petersen Shay K + Moreau RF + Smith EJ + Hagen TM. - + + 16011463 + PubMed + Vitamin E, oxidative stress, and inflammation. + Annu Rev Nutr. + 2005 + Singh U + Devaraj S + Jialal I. + + - Prostaglandin and Leukotriene Metabolism - Ingenuity software - https://analysis.ingenuity.com/pa/ + Arachidonic Acid Metabolism + Ingenuity sofware + https://analysis.ingenuity.com/ + + + 16047261 + PubMed + Homocysteine: overview of biochemistry, molecular biology, and role in disease processes. + Semin Vasc Med + 2005 + Fowler B. 8968737 @@ -2666,14 +2696,6 @@ Rozen R Gravel RA. - - 10448523 - PubMed - Homocysteine metabolism. - Annu Rev Nutr - 1999 - Selhub J. - 10444342 PubMed @@ -2682,83 +2704,72 @@ 1999 Wilson A, Platt R, Wu Q, Leclerc D, Christensen B, Yang H, Gravel RA, Rozen R + + 840498 + PubMed + Cystathionine beta-synthase deficiency: a qualitative abnormality of the deficient enzyme modified by vitamin B6 therapy. + Pediatr Res. + 1977 + Longhi RC + Fleisher LD + Tallan HH + Gaull GE. + pathway of folate cycle/metabolism PW:0000140 Pathway Ontology - - - - Folic acid - Linus Pauling Institute - http://lpi.oregonstate.edu/infocenter/vitamins/fa/ - - - 14726604 + + 18466421 PubMed - Nitric oxide and superoxide in inflammation and immune regulation. - J Physiol Pharmacol. - 2003 - Guzik TJ - Korbut R - Adamek-Guzik T. - - - 978-0-309-06411-8 - ISBN - Food and Nutrition Board, Institute of Medicine. Vitamin B6. Dietary Reference Intakes: Thiamin, Riboflavin, Niacin, Vitamin B6, Vitamin B12, Pantothenic Acid, Biotin, and Choline. - Washington D.C.: National Academies Press - 1998 + The role of urate and xanthine oxidase inhibitors in cardiovascular disease. + Cardiovasc Ther. + 2008 + George J + Struthers AD. - - 18409172 + + 18598592 PubMed - Is alpha-lipoic acid a scavenger of reactive oxygen species in vivo? Evidence for its initiation of stress signaling pathways that promote endogenous antioxidant capacity. - IUBMB Life. + A network biology model of micronutrient related health + Br J Nutr 2008 - Petersen Shay K - Moreau RF - Smith EJ - Hagen TM. + Ben van Ommen + Susan Fairweather-Tait + Andreas Freidig + Alwine Kardinaal + Augustin Scalbert + Suzan Wopereis - - 16962588 - PubMed - Identification and characterization of selenoprotein K: an antioxidant in cardiomyocytes. - FEBS Lett. - 2006 - Lu C - Qiu F - Zhou H - Peng Yp - Hao W - Xu J - Yuan J - Wang S - Qiang B - Xu C - Peng X. + + + + Prostaglandin and Leukotriene Metabolism + Ingenuity software + https://analysis.ingenuity.com/pa/ - - 10.1021/bi981808n - DOI - Binding of Pyridoxal 5'-Phosphate to the Heme Protein Human Cystathionine β-Synthase - Biochemistry 38(9) - 1999 - Vladimir Kery - Loelle Poneleit - Jeffrey D. Meyer - Mark C. Manning - Jan P. Kraus + + + + Vitamin B 6 + Linus Paulin institute + http://lpi.oregonstate.edu/infocenter/vitamins/vitaminB6/ - - 6295699 + + WP28 + WikiPathways + Selenoproteins + http://www.wikipathways.org/index.php/Pathway:Homo_sapiens:Selenoproteins + WikiPathways + + + 8846925 PubMed - Vitamin B12 binders (transcobalamins) in serum. - Crit Rev Clin Lab Sci. - 1982 - Fernandes-Costa F: Metz J. + Free radicals, uric acid, and human disease. + Free Radic Biol Med. + 1996 + Proctor PH. 6300970 @@ -2776,25 +2787,36 @@ Larue M Rokach J. - - WP28 - WikiPathways - Selenoproteins - http://www.wikipathways.org/index.php/Pathway:Homo_sapiens:Selenoproteins - WikiPathways + + 11731805 + PubMed + Domain alternation switches B(12)-dependent methionine synthase to the activation conformation. + Nat Struct Biol. + 2002 + Bandarian V + Pattridge KA + Lennon BW + Huddler DP + Matthews RG + Ludwig ML. - - 18598592 + + 16962588 PubMed - A network biology model of micronutrient related health - Br J Nutr - 2008 - Ben van Ommen - Susan Fairweather-Tait - Andreas Freidig - Alwine Kardinaal - Augustin Scalbert - Suzan Wopereis + Identification and characterization of selenoprotein K: an antioxidant in cardiomyocytes. + FEBS Lett. + 2006 + Lu C + Qiu F + Zhou H + Peng Yp + Hao W + Xu J + Yuan J + Wang S + Qiang B + Xu C + Peng X. @@ -2803,24 +2825,23 @@ Ingenuity software https://analysis.ingenuity.com/ - - 840498 + + 10448523 PubMed - Cystathionine beta-synthase deficiency: a qualitative abnormality of the deficient enzyme modified by vitamin B6 therapy. - Pediatr Res. - 1977 - Longhi RC - Fleisher LD - Tallan HH - Gaull GE. + Homocysteine metabolism. + Annu Rev Nutr + 1999 + Selhub J. - - 16047261 + + 14726604 PubMed - Homocysteine: overview of biochemistry, molecular biology, and role in disease processes. - Semin Vasc Med - 2005 - Fowler B. + Nitric oxide and superoxide in inflammation and immune regulation. + J Physiol Pharmacol. + 2003 + Guzik TJ + Korbut R + Adamek-Guzik T. 1184739 @@ -2830,48 +2851,24 @@ 1975 Hall CA - - 18466421 - PubMed - The role of urate and xanthine oxidase inhibitors in cardiovascular disease. - Cardiovasc Ther. - 2008 - George J - Struthers AD. - - - 8846925 - PubMed - Free radicals, uric acid, and human disease. - Free Radic Biol Med. - 1996 - Proctor PH. - - - 16011463 - PubMed - Vitamin E, oxidative stress, and inflammation. - Annu Rev Nutr. - 2005 - Singh U - Devaraj S - Jialal I. - - + - Arachidonic Acid Metabolism - Ingenuity sofware - https://analysis.ingenuity.com/ + Folic acid + Linus Pauling Institute + http://lpi.oregonstate.edu/infocenter/vitamins/fa/ - - 8534261 - PubMed - The isoprostanes. Current knowledge and directions for future research. - Biochem Pharmacol. - 1996 - Morrow JD - Roberts LJ 2nd. + + 10.1021/bi981808n + DOI + Binding of Pyridoxal 5'-Phosphate to the Heme Protein Human Cystathionine β-Synthase + Biochemistry 38(9) + 1999 + Vladimir Kery + Loelle Poneleit + Jeffrey D. Meyer + Mark C. Manning + Jan P. Kraus 15104204 @@ -2881,18 +2878,21 @@ 2004 Basu S. - - 11731805 + + 10448523 PubMed - Domain alternation switches B(12)-dependent methionine synthase to the activation conformation. - Nat Struct Biol. - 2002 - Bandarian V - Pattridge KA - Lennon BW - Huddler DP - Matthews RG - Ludwig ML. + Homocysteine metabolism. + Annu Rev Nutr. + 1999 + Selhub J. + + + 6295699 + PubMed + Vitamin B12 binders (transcobalamins) in serum. + Crit Rev Clin Lab Sci. + 1982 + Fernandes-Costa F: Metz J. diff --git a/pathways/WP1311/WP1311.json b/pathways/WP1311/WP1311.json index 0cad28400..6a1939cc2 100644 --- a/pathways/WP1311/WP1311.json +++ b/pathways/WP1311/WP1311.json @@ -22873,7 +22873,7 @@ "id": "publicationXrefa21", "source": "FEBS Lett.", "standardName": "Identification and characterization of selenoprotein K: an antioxidant in cardiomyocytes.", - "textContent": "22", + "textContent": "21", "type": [ "PublicationXref", "PubMed:16962588" @@ -22894,7 +22894,7 @@ "id": "publicationXrefa49", "source": "Biochemistry 38(9)", "standardName": "Binding of Pyridoxal 5'-Phosphate to the Heme Protein Human Cystathionine β-Synthase", - "textContent": "16", + "textContent": "11", "type": [ "PublicationXref", "DOI:10.1021/bi981808n" @@ -22914,7 +22914,7 @@ "id": "publicationXrefa58", "source": "IUBMB Life.", "standardName": "Is alpha-lipoic acid a scavenger of reactive oxygen species in vivo? Evidence for its initiation of stress signaling pathways that promote endogenous antioxidant capacity.", - "textContent": "23", + "textContent": "18", "type": [ "PublicationXref", "PubMed:18409172" @@ -22932,7 +22932,7 @@ "id": "publicationXrefa62", "source": "Biochem Pharmacol.", "standardName": "The isoprostanes. Current knowledge and directions for future research.", - "textContent": "14", + "textContent": "5", "type": [ "PublicationXref", "PubMed:8534261" @@ -22949,7 +22949,7 @@ "id": "publicationXrefa89", "source": "Ingenuity software", "standardName": "Prostaglandin and Leukotriene Metabolism", - "textContent": "4", + "textContent": "24", "type": [ "PublicationXref" ] @@ -22962,7 +22962,7 @@ "id": "publicationXrefb83", "source": "Linus Pauling Institute", "standardName": "Folic acid", - "textContent": "11", + "textContent": "28", "type": [ "PublicationXref" ] @@ -22972,7 +22972,7 @@ "id": "publicationXrefb89", "source": "Washington D.C.: National Academies Press", "standardName": "Food and Nutrition Board, Institute of Medicine. Vitamin B6. Dietary Reference Intakes: Thiamin, Riboflavin, Niacin, Vitamin B6, Vitamin B12, Pantothenic Acid, Biotin, and Choline.", - "textContent": "15", + "textContent": "8", "type": [ "PublicationXref", "ISBN:978-0-309-06411-8" @@ -22997,7 +22997,7 @@ "id": "publicationXrefbbd", "source": "Prostaglandins.", "standardName": "Synthesis and biological activities of leukotriene F4 and leukotriene F4 sulfone", - "textContent": "7", + "textContent": "3", "type": [ "PublicationXref", "PubMed:6300970" @@ -23017,7 +23017,7 @@ "id": "publicationXrefbc2", "source": "Pediatr Res.", "standardName": "Cystathionine beta-synthase deficiency: a qualitative abnormality of the deficient enzyme modified by vitamin B6 therapy.", - "textContent": "12", + "textContent": "2", "type": [ "PublicationXref", "PubMed:840498" @@ -23039,7 +23039,7 @@ "id": "publicationXrefc1b", "source": "Br J Nutr", "standardName": "A network biology model of micronutrient related health", - "textContent": "25", + "textContent": "23", "type": [ "PublicationXref", "PubMed:18598592" @@ -23060,7 +23060,7 @@ "id": "publicationXrefc1e", "source": "Proc Natl Acad Sci U S A.", "standardName": "Selenoprotein R is a zinc-containing stereo-specific methionine sulfoxide reductase.", - "textContent": "2", + "textContent": "13", "type": [ "PublicationXref", "PubMed:11929995" @@ -23077,7 +23077,7 @@ "id": "publicationXrefca8", "source": "Molecular genetics and metabolism", "standardName": "A common variant in methionine synthase reductase combined with low cobalamin (vitamin B12) increases risk for spina bifida.", - "textContent": "10", + "textContent": "9", "type": [ "PublicationXref", "PubMed:10444342" @@ -23099,7 +23099,7 @@ "id": "publicationXrefcbd", "source": "Nat Struct Biol.", "standardName": "Domain alternation switches B(12)-dependent methionine synthase to the activation conformation.", - "textContent": "17", + "textContent": "14", "type": [ "PublicationXref", "PubMed:11731805" @@ -23125,7 +23125,7 @@ "id": "publicationXrefcc4", "source": "Hum Mol Genet.", "standardName": "Human methionine synthase: cDNA cloning and identification of mutations in patients of the cblG complementation group of folate/cobalamin disorders.", - "textContent": "8", + "textContent": "6", "type": [ "PublicationXref", "PubMed:8968737" @@ -23159,7 +23159,7 @@ "id": "publicationXrefce8", "source": "Free Radic Res.", "standardName": "Isoprostanes: novel bioactive products of lipid peroxidation.", - "textContent": "19", + "textContent": "16", "type": [ "PublicationXref", "PubMed:15104204" @@ -23176,7 +23176,7 @@ "id": "publicationXrefcf3", "source": "Annu Rev Nutr", "standardName": "Homocysteine metabolism.", - "textContent": "9", + "textContent": "10", "type": [ "PublicationXref", "PubMed:10448523" @@ -23193,7 +23193,7 @@ "id": "publicationXrefdab", "source": "Crit Rev Clin Lab Sci.", "standardName": "Vitamin B12 binders (transcobalamins) in serum.", - "textContent": "6", + "textContent": "4", "type": [ "PublicationXref", "PubMed:6295699" @@ -23212,7 +23212,7 @@ "id": "publicationXrefdc8", "source": "Annu Rev Nutr.", "standardName": "Vitamin E, oxidative stress, and inflammation.", - "textContent": "21", + "textContent": "17", "type": [ "PublicationXref", "PubMed:16011463" @@ -23229,7 +23229,7 @@ "id": "publicationXrefe10", "source": "The Journal of clinical investigation", "standardName": "Transcobalamins I and II as natural transport proteins of vitamin B12.", - "textContent": "5", + "textContent": "1", "type": [ "PublicationXref", "PubMed:1184739" @@ -23246,7 +23246,7 @@ "id": "publicationXrefe80", "source": "Linus Paulin institute", "standardName": "Vitamin B 6", - "textContent": "3", + "textContent": "25", "type": [ "PublicationXref" ] @@ -23261,7 +23261,7 @@ "id": "publicationXrefebb", "source": "J Physiol Pharmacol.", "standardName": "Nitric oxide and superoxide in inflammation and immune regulation.", - "textContent": "18", + "textContent": "15", "type": [ "PublicationXref", "PubMed:14726604" @@ -23278,7 +23278,7 @@ "id": "publicationXrefec3", "source": "http://www.wikipathways.org/index.php/Pathway:Homo_sapiens:Selenoproteins", "standardName": "Selenoproteins", - "textContent": "24", + "textContent": "26", "type": [ "PublicationXref", "WikiPathways:WP28" @@ -23295,7 +23295,7 @@ "id": "publicationXrefed9", "source": "Cardiovasc Ther.", "standardName": "The role of urate and xanthine oxidase inhibitors in cardiovascular disease.", - "textContent": "27", + "textContent": "22", "type": [ "PublicationXref", "PubMed:18466421" @@ -23312,7 +23312,7 @@ "id": "publicationXreff15", "source": "Free Radic Biol Med.", "standardName": "Free radicals, uric acid, and human disease.", - "textContent": "13", + "textContent": "7", "type": [ "PublicationXref", "PubMed:8846925" @@ -23329,7 +23329,7 @@ "id": "publicationXreff1b", "source": "Annu Rev Nutr.", "standardName": "Homocysteine metabolism.", - "textContent": "1", + "textContent": "12", "type": [ "PublicationXref", "PubMed:10448523" @@ -23346,7 +23346,7 @@ "id": "publicationXreff96", "source": "Ingenuity software", "standardName": "Prostaglandin and Leukotriene Metabolism", - "textContent": "26", + "textContent": "27", "type": [ "PublicationXref" ] @@ -23359,7 +23359,7 @@ "id": "publicationXrefff2", "source": "Ingenuity sofware", "standardName": "Arachidonic Acid Metabolism", - "textContent": "28", + "textContent": "19", "type": [ "PublicationXref" ] diff --git a/pathways/WP1765/WP1765.gpml b/pathways/WP1765/WP1765.gpml index 0c887c8e9..c578a6785 100644 --- a/pathways/WP1765/WP1765.gpml +++ b/pathways/WP1765/WP1765.gpml @@ -174,11 +174,6 @@ - - mechanotransduction pathway - PW:0001502 - Pathway Ontology - 12750328 PubMed @@ -193,6 +188,11 @@ PW:0000003 Pathway Ontology + + mechanotransduction pathway + PW:0001502 + Pathway Ontology + diff --git a/pathways/WP1765/WP1765.json b/pathways/WP1765/WP1765.json index a40d932b6..a5fea13de 100644 --- a/pathways/WP1765/WP1765.json +++ b/pathways/WP1765/WP1765.json @@ -1624,8 +1624,8 @@ "textContent": "Name: Mechanosensory inputs influence pharyngeal activity via ivermectin sensitivity genes\nLast Modified: 20240716191846\nOrganism: Caenorhabditis elegans", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0001502", - "http://identifiers.org/pw/PW:0000003" + "http://identifiers.org/pw/PW:0000003", + "http://identifiers.org/pw/PW:0001502" ], "verticalAlign": "top", "width": 620, diff --git a/pathways/WP2197/WP2197.gpml b/pathways/WP2197/WP2197.gpml index d89be4e99..df2e09cad 100644 --- a/pathways/WP2197/WP2197.gpml +++ b/pathways/WP2197/WP2197.gpml @@ -1247,45 +1247,40 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - calcium/calmodulin dependent signaling pathway - PW:0000314 - Pathway Ontology - benign essential hypertension DOID:10913 Disease - G protein mediated signaling pathway via Galphai family - PW:0000228 + G protein mediated signaling pathway via Galphas family + PW:0000227 Pathway Ontology - Ras superfamily mediated signaling pathway - PW:0000006 + G protein mediated signaling pathway via Galphaq family + PW:0000229 Pathway Ontology + + blood vessel endothelial cell + CL:0000071 + Cell Type + endothelin signaling pathway PW:0000506 Pathway Ontology - smooth muscle cell - CL:0000192 - Cell Type - - - G protein mediated signaling pathway via Galphaq family - PW:0000229 + Ras superfamily mediated signaling pathway + PW:0000006 Pathway Ontology - G protein mediated signaling pathway via Galphas family - PW:0000227 - Pathway Ontology + smooth muscle cell + CL:0000192 + Cell Type hypertension @@ -1293,9 +1288,14 @@ Proteins on this pathway have targeted assays available via the [https://assays. Disease - blood vessel endothelial cell - CL:0000071 - Cell Type + G protein mediated signaling pathway via Galphai family + PW:0000228 + Pathway Ontology + + + calcium/calmodulin dependent signaling pathway + PW:0000314 + Pathway Ontology diff --git a/pathways/WP2197/WP2197.json b/pathways/WP2197/WP2197.json index af0e77a6a..efa6eba9c 100644 --- a/pathways/WP2197/WP2197.json +++ b/pathways/WP2197/WP2197.json @@ -11757,12 +11757,12 @@ "textContent": "Name: Endothelin pathways\nLast Modified: 20240716192253\nOrganism: Homo sapiens", "type": [ "Pathway", - "http://identifiers.org/pw/PW:0000314", - "http://identifiers.org/pw/PW:0000228", - "http://identifiers.org/pw/PW:0000006", - "http://identifiers.org/pw/PW:0000506", + "http://identifiers.org/pw/PW:0000227", "http://identifiers.org/pw/PW:0000229", - "http://identifiers.org/pw/PW:0000227" + "http://identifiers.org/pw/PW:0000506", + "http://identifiers.org/pw/PW:0000006", + "http://identifiers.org/pw/PW:0000228", + "http://identifiers.org/pw/PW:0000314" ], "verticalAlign": "top", "width": 1789.9841124263874, diff --git a/pathways/WP2199/WP2199-bibliography.tsv b/pathways/WP2199/WP2199-bibliography.tsv index a367795fa..b72667f90 100644 --- a/pathways/WP2199/WP2199-bibliography.tsv +++ b/pathways/WP2199/WP2199-bibliography.tsv @@ -1,82 +1,82 @@ ID Database Citation -8193305 Pubmed "Hattori T, Terada T, Hamasuna ST. Sequence and functional analyses of the rice gene homologous to the maize Vp1. Plant Mol Biol. 1994 Mar;24(5):805–10. PubMed Europe PMC Scholia" -8940135 Pubmed "Nantel A, Quatrano RS. Characterization of three rice basic/leucine zipper factors, including two inhibitors of EmBP-1 DNA binding activity. J Biol Chem. 1996 Dec 6;271(49):31296–305. PubMed Europe PMC Scholia" -9596641 Pubmed "Schultz TF, Medina J, Hill A, Quatrano RS. 14-3-3 proteins are part of an abscisic acid-VIVIPAROUS1 (VP1) response complex in the Em promoter and interact with VP1 and EmBP1. Plant Cell. 1998 May;10(5):837–47. PubMed Europe PMC Scholia" -10417713 Pubmed "Kawasaki T, Okumura S, Kishimoto N, Shimada H, Higo K, Ichikawa N. RNA maturation of the rice SPK gene may involve trans-splicing. Plant J. 1999 Jun;18(6):625–32. PubMed Europe PMC Scholia" -10805599 Pubmed "Chae HS, Cho YG, Park MY, Lee MC, Eun MY, Kang BG, et al. Hormonal cross-talk between auxin and ethylene differentially regulates the expression of two members of the 1-aminocyclopropane-1-carboxylate oxidase gene family in rice (Oryza sativa L.). Plant Cell Physiol. 2000 Mar;41(3):354–62. PubMed Europe PMC Scholia" -10987556 Pubmed "Fabian T, Lorbiecke R, Umeda M, Sauter M. The cell cycle genes cycA1;1 and cdc2Os-3 are coordinately regulated by gibberellin in planta. Planta. 2000 Aug;211(3):376–83. PubMed Europe PMC Scholia" -11910009 Pubmed "Asano T, Kunieda N, Omura Y, Ibe H, Kawasaki T, Takano M, et al. Rice SPK, a calmodulin-like domain protein kinase, is required for storage product accumulation during seed development: phosphorylation of sucrose synthase is a possible factor. Plant Cell. 2002 Mar;14(3):619–28. PubMed Europe PMC Scholia" -12684538 Pubmed "Cooper B, Clarke JD, Budworth P, Kreps J, Hutchison D, Park S, et al. A network of rice genes associated with stress response and seed development. Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4945–50. PubMed Europe PMC Scholia" -12783325 Pubmed "Yamamoto T, Kimura S, Mori Y, Uchiyama Y, Ishibashi T, Hashimoto J, et al. Interaction between proliferating cell nuclear antigen and JUN-activation-domain-binding protein 1 in the meristem of rice, Oryza sativa L. Planta. 2003 Jun;217(2):175–83. PubMed Europe PMC Scholia" -12947109 Pubmed "Zhu Y, Cai X-L, Wang Z-Y, Hong M-M. An interaction between a MYC protein and an EREBP protein is involved in transcriptional regulation of the rice Wx gene. J Biol Chem. 2003 Nov 28;278(48):47803–11. PubMed Europe PMC Scholia" -14733924 Pubmed "Yamamoto T, Mori Y, Ishibashi T, Uchiyama Y, Sakaguchi N, Furukawa T, et al. Characterization of Rad6 from a higher plant, rice (Oryza sativa L.) and its interaction with Sgt1, a subunit of the SCF ubiquitin ligase complex. Biochem Biophys Res Commun. 2004 Feb 6;314(2):434–9. PubMed Europe PMC Scholia" -15047897 Pubmed "Zhang Z-L, Xie Z, Zou X, Casaretto J, Ho T-HD, Shen QJ. A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Plant Physiol. 2004 Apr;134(4):1500–13. PubMed Europe PMC Scholia" -15220467 Pubmed "Wong HL, Sakamoto T, Kawasaki T, Umemura K, Shimamoto K. Down-regulation of metallothionein, a reactive oxygen scavenger, by the small GTPase OsRac1 in rice. Plant Physiol. 2004 Jul;135(3):1447–56. PubMed Europe PMC Scholia" -15232694 Pubmed "Hirose T, Terao T. A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). Planta. 2004 Nov;220(1):9–16. PubMed Europe PMC Scholia" -15356337 Pubmed "Shimada H, Koishihara H, Saito Y, Arashima Y, Furukawa T, Hayashi H. A rice antisense SPK transformant that lacks the accumulation of seed storage substances shows no correlation between sucrose concentration in phloem sap and demand for carbon sources in the sink organs. Plant Cell Physiol. 2004 Aug;45(8):1105–9. PubMed Europe PMC Scholia" -15759120 Pubmed "Cho J-I, Lee S-K, Ko S, Kim H-K, Jun S-H, Lee Y-H, et al. Molecular cloning and expression analysis of the cell-wall invertase gene family in rice (Oryza sativa L.). Plant Cell Rep. 2005 Jun;24(4):225–36. PubMed Europe PMC Scholia" -15806324 Pubmed "Yamamoto T, Mori Y, Ishibashi T, Uchiyama Y, Ueda T, Ando T, et al. Interaction between proliferating cell nuclear antigen (PCNA) and a DnaJ induced by DNA damage. J Plant Res. 2005 Apr;118(2):91–7. PubMed Europe PMC Scholia" -15891897 Pubmed "Kasai K, Kanno T, Akita M, Ikejiri-Kanno Y, Wakasa K, Tozawa Y. Identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins. Planta. 2005 Oct;222(3):438–47. PubMed Europe PMC Scholia" -15976269 Pubmed "Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, et al. Cytokinin oxidase regulates rice grain production. Science. 2005 Jul 29;309(5735):741–5. PubMed Europe PMC Scholia" -16152656 Pubmed "Komatsu S, Abbasi F, Kobori E, Fujisawa Y, Kato H, Iwasaki Y. Proteomic analysis of rice embryo: an approach for investigating Galpha protein-regulated proteins. Proteomics. 2005 Oct;5(15):3932–41. PubMed Europe PMC Scholia" -16275672 Pubmed "Ohdan T, Francisco PB Jr, Sawada T, Hirose T, Terao T, Satoh H, et al. Expression profiling of genes involved in starch synthesis in sink and source organs of rice. J Exp Bot. 2005 Dec;56(422):3229–44. PubMed Europe PMC Scholia" -16436304 Pubmed "Cao Y, Song F, Goodman RM, Zheng Z. Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress. J Plant Physiol. 2006 Nov;163(11):1167–78. PubMed Europe PMC Scholia" -16623886 Pubmed "Xie Z, Zhang Z-L, Zou X, Yang G, Komatsu S, Shen QJ. Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. Plant J. 2006 Apr;46(2):231–42. PubMed Europe PMC Scholia" -16667159 Pubmed "Hahn M, Walbot V. Effects of cold-treatment on protein synthesis and mRNA levels in rice leaves. Plant Physiol. 1989 Nov;91(3):930–8. PubMed Europe PMC Scholia" -16786297 Pubmed "Mao C, Wang S, Jia Q, Wu P. OsEIL1, a rice homolog of the Arabidopsis EIN3 regulates the ethylene response as a positive component. Plant Mol Biol. 2006 May;61(1–2):141–52. PubMed Europe PMC Scholia" -16798940 Pubmed "Yamamoto MP, Onodera Y, Touno SM, Takaiwa F. Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes. Plant Physiol. 2006 Aug;141(4):1694–707. PubMed Europe PMC Scholia" -16896230 Pubmed "Li X, Duan X, Jiang H, Sun Y, Tang Y, Yuan Z, et al. Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Plant Physiol. 2006 Aug;141(4):1167–84. PubMed Europe PMC Scholia" -16953433 Pubmed "Utsumi Y, Nakamura Y. Structural and enzymatic characterization of the isoamylase1 homo-oligomer and the isoamylase1-isoamylase2 hetero-oligomer from rice endosperm. Planta. 2006 Dec;225(1):75–87. PubMed Europe PMC Scholia" -17297616 Pubmed "Ryoo N, Yu C, Park C-S, Baik M-Y, Park IM, Cho M-H, et al. Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.). Plant Cell Rep. 2007 Jul;26(7):1083–95. PubMed Europe PMC Scholia" -17339651 Pubmed "Rzewuski G, Cornell KA, Rooney L, Bürstenbinder K, Wirtz M, Hell R, et al. OsMTN encodes a 5’-methylthioadenosine nucleosidase that is up-regulated during submergence-induced ethylene synthesis in rice (Oryza sativa L.). J Exp Bot. 2007;58(6):1505–14. PubMed Europe PMC Scholia" -17376611 Pubmed "Kang SG, Jeong HK, Lee E, Natarajan S. Characterization of a lipoate-protein ligase A gene of rice (Oryza sativa L.). Gene. 2007 May 15;393(1–2):53–61. PubMed Europe PMC Scholia" -17384160 Pubmed "Yamakawa H, Hirose T, Kuroda M, Yamaguchi T. Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. Plant Physiol. 2007 May;144(1):258–77. PubMed Europe PMC Scholia" -17406793 Pubmed "Lee S-K, Hwang S-K, Han M, Eom J-S, Kang H-G, Han Y, et al. Identification of the ADP-glucose pyrophosphorylase isoforms essential for starch synthesis in the leaf and seed endosperm of rice (Oryza sativa L.). Plant Mol Biol. 2007 Nov;65(4):531–46. PubMed Europe PMC Scholia" -17426956 Pubmed "Xiao B, Huang Y, Tang N, Xiong L. Over-expression of a LEA gene in rice improves drought resistance under the field conditions. Theor Appl Genet. 2007 Jun;115(1):35–46. PubMed Europe PMC Scholia" -17559517 Pubmed "Ogo Y, Itai RN, Nakanishi H, Kobayashi T, Takahashi M, Mori S, et al. The rice bHLH protein OsIRO2 is an essential regulator of the genes involved in Fe uptake under Fe-deficient conditions. Plant J. 2007 Aug;51(3):366–77. PubMed Europe PMC Scholia" -17579813 Pubmed "Zeng D, Yan M, Wang Y, Liu X, Qian Q, Li J. Du1, encoding a novel Prp1 protein, regulates starch biosynthesis through affecting the splicing of Wxb pre-mRNAs in rice (Oryza sativa L.). Plant Mol Biol. 2007 Nov;65(4):501–9. PubMed Europe PMC Scholia" -17587305 Pubmed "Nakashima K, Tran L-SP, Van Nguyen D, Fujita M, Maruyama K, Todaka D, et al. Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Plant J. 2007 Aug;51(4):617–30. PubMed Europe PMC Scholia" -17604002 Pubmed "Zou M, Guan Y, Ren H, Zhang F, Chen F. Characterization of alternative splicing products of bZIP transcription factors OsABI5. Biochem Biophys Res Commun. 2007 Aug 24;360(2):307–13. PubMed Europe PMC Scholia" -17640358 Pubmed "Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, et al. MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. BMC Genomics. 2007 Jul 18;8:242. PubMed Europe PMC Scholia" -18025467 Pubmed "Kobayashi T, Ogo Y, Itai RN, Nakanishi H, Takahashi M, Mori S, et al. The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants. Proc Natl Acad Sci U S A. 2007 Nov 27;104(48):19150–5. PubMed Europe PMC Scholia" -18156216 Pubmed "Thao NP, Chen L, Nakashima A, Hara S, Umemura K, Takahashi A, et al. RAR1 and HSP90 form a complex with Rac/Rop GTPase and function in innate-immune responses in rice. Plant Cell. 2007 Dec;19(12):4035–45. PubMed Europe PMC Scholia" -18257679 Pubmed "Wang Y, Gao M, Li Q, Wang L, Wang J, Jeon J-S, et al. OsRAR1 and OsSGT1 physically interact and function in rice basal disease resistance. Mol Plant Microbe Interact. 2008 Mar;21(3):294–303. PubMed Europe PMC Scholia" -18308732 Pubmed "Ogo Y, Kobayashi T, Nakanishi Itai R, Nakanishi H, Kakei Y, Takahashi M, et al. A novel NAC transcription factor, IDEF2, that recognizes the iron deficiency-responsive element 2 regulates the genes involved in iron homeostasis in plants. J Biol Chem. 2008 May 9;283(19):13407–17. PubMed Europe PMC Scholia" -18315698 Pubmed "Shobbar Z-S, Oane R, Gamuyao R, De Palma J, Malboobi MA, Karimzadeh G, et al. Abscisic acid regulates gene expression in cortical fiber cells and silica cells of rice shoots. New Phytol. 2008;178(1):68–79. PubMed Europe PMC Scholia" -18454147 Pubmed "Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, et al. Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet. 2008 Jun;40(6):761–7. PubMed Europe PMC Scholia" -18599581 Pubmed "Chen S, Yang Y, Shi W, Ji Q, He F, Zhang Z, et al. Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Plant Cell. 2008 Jul;20(7):1850–61. PubMed Europe PMC Scholia" -18713381 Pubmed "Wang Y-Q, Wei X-L, Xu H-L, Chai C-L, Meng K, Zhai H-L, et al. Cell-wall invertases from rice are differentially expressed in Caryopsis during the grain filling stage. J Integr Plant Biol. 2008 Apr;50(4):466–74. PubMed Europe PMC Scholia" -18723578 Pubmed "Nakashima A, Chen L, Thao NP, Fujiwara M, Wong HL, Kuwano M, et al. RACK1 functions in rice innate immunity by interacting with the Rac1 immune complex. Plant Cell. 2008 Aug;20(8):2265–79. PubMed Europe PMC Scholia" -18755073 Pubmed "Cho JH, Kim HB, Kim H-S, Choi S-B. Identification and characterization of a rice MCM2 homologue required for DNA replication. BMB Rep. 2008 Aug 31;41(8):581–6. PubMed Europe PMC Scholia" -18820698 Pubmed "Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, et al. Control of rice grain-filling and yield by a gene with a potential signature of domestication. Nat Genet. 2008 Nov;40(11):1370–4. PubMed Europe PMC Scholia" -18826428 Pubmed "Umemura K, Satou J, Iwata M, Uozumi N, Koga J, Kawano T, et al. Contribution of salicylic acid glucosyltransferase, OsSGT1, to chemically induced disease resistance in rice plants. Plant J. 2009 Feb;57(3):463–72. PubMed Europe PMC Scholia" -18840300 Pubmed "Niu X, Tang W, Huang W, Ren G, Wang Q, Luo D, et al. RNAi-directed downregulation of OsBADH2 results in aroma (2-acetyl-1-pyrroline) production in rice (Oryza sativa L.). BMC Plant Biol. 2008 Oct 8;8:100. PubMed Europe PMC Scholia" -19015668 Pubmed "Weng J, Gu S, Wan X, Gao H, Guo T, Su N, et al. Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res. 2008 Dec;18(12):1199–209. PubMed Europe PMC Scholia" -19052152 Pubmed "Shin J-H, Kim S-R, An G. Rice aldehyde dehydrogenase7 is needed for seed maturation and viability. Plant Physiol. 2009 Feb;149(2):905–15. PubMed Europe PMC Scholia" -19266169 Pubmed "Song Y, You J, Xiong L. Characterization of OsIAA1 gene, a member of rice Aux/IAA family involved in auxin and brassinosteroid hormone responses and plant morphogenesis. Plant Mol Biol. 2009 Jun;70(3):297–309. PubMed Europe PMC Scholia" -19321714 Pubmed "Radchuk VV, Borisjuk L, Sreenivasulu N, Merx K, Mock H-P, Rolletschek H, et al. Spatiotemporal profiling of starch biosynthesis and degradation in the developing barley grain. Plant Physiol. 2009 May;150(1):190–204. PubMed Europe PMC Scholia" -19429605 Pubmed "Oh S-J, Kim YS, Kwon C-W, Park HK, Jeong JS, Kim J-K. Overexpression of the transcription factor AP37 in rice improves grain yield under drought conditions. Plant Physiol. 2009 Jul;150(3):1368–79. PubMed Europe PMC Scholia" -19473328 Pubmed "Kawakatsu T, Yamamoto MP, Touno SM, Yasuda H, Takaiwa F. Compensation and interaction between RISBZ1 and RPBF during grain filling in rice. Plant J. 2009 Sep;59(6):908–20. PubMed Europe PMC Scholia" -19490115 Pubmed "Jain M, Khurana JP. Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS J. 2009 Jun;276(11):3148–62. PubMed Europe PMC Scholia" -19506305 Pubmed "Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, et al. Evolutionary history of GS3, a gene conferring grain length in rice. Genetics. 2009 Aug;182(4):1323–34. PubMed Europe PMC Scholia" -19593540 Pubmed "Yan H-B, Pan X-X, Jiang H-W, Wu G-J. Comparison of the starch synthesis genes between maize and rice: copies, chromosome location and expression divergence. Theor Appl Genet. 2009 Sep;119(5):815–25. PubMed Europe PMC Scholia" -19682292 Pubmed "Bi Y-M, Kant S, Clarke J, Gidda S, Ming F, Xu J, et al. Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling. Plant Cell Environ. 2009 Dec;32(12):1749–60. PubMed Europe PMC Scholia" -19737364 Pubmed "Kobayashi T, Itai RN, Ogo Y, Kakei Y, Nakanishi H, Takahashi M, et al. The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes. Plant J. 2009 Dec;60(6):948–61. PubMed Europe PMC Scholia" -19807881 Pubmed "Ji H, Kim S-R, Kim Y-H, Kim H, Eun M-Y, Jin I-D, et al. Inactivation of the CTD phosphatase-like gene OsCPL1 enhances the development of the abscission layer and seed shattering in rice. Plant J. 2010 Jan;61(1):96–106. PubMed Europe PMC Scholia" -19921249 Pubmed "Guo J, Wang F, Song J, Sun W, Zhang XS. The expression of Orysa;CycB1;1 is essential for endosperm formation and causes embryo enlargement in rice. Planta. 2010 Jan;231(2):293–303. PubMed Europe PMC Scholia" -19933315 Pubmed "Mizutani M, Naganuma T, Tsutsumi K, Saitoh Y. The syncytium-specific expression of the Orysa;KRP3 CDK inhibitor: implication of its involvement in the cell cycle control in the rice (Oryza sativa L.) syncytial endosperm. J Exp Bot. 2010 Mar;61(3):791–8. PubMed Europe PMC Scholia" -20220098 Pubmed "Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, et al. Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5792–7. PubMed Europe PMC Scholia" -20305271 Pubmed "Nakamura Y, Utsumi Y, Sawada T, Aihara S, Utsumi C, Yoshida M, et al. Characterization of the reactions of starch branching enzymes from rice endosperm. Plant Cell Physiol. 2010 May;51(5):776–94. PubMed Europe PMC Scholia" -20335401 Pubmed "Jeong JS, Kim YS, Baek KH, Jung H, Ha S-H, Do Choi Y, et al. Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiol. 2010 May;153(1):185–97. PubMed Europe PMC Scholia" -20416079 Pubmed "Wang E, Xu X, Zhang L, Zhang H, Lin L, Wang Q, et al. Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. BMC Evol Biol. 2010 Apr 23;10:108. PubMed Europe PMC Scholia" -20460361 Pubmed "Sun S-J, Guo S-Q, Yang X, Bao Y-M, Tang H-J, Sun H, et al. Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice. J Exp Bot. 2010 Jun;61(10):2807–18. PubMed Europe PMC Scholia" -20478538 Pubmed "Kawano Y, Akamatsu A, Hayashi K, Housen Y, Okuda J, Yao A, et al. Activation of a Rac GTPase by the NLR family disease resistance protein Pit plays a critical role in rice innate immunity. Cell Host Microbe. 2010 May 20;7(5):362–75. PubMed Europe PMC Scholia" -20490919 Pubmed "Yi N, Oh S-J, Kim YS, Jang H-J, Park S-H, Jeong JS, et al. Analysis of the Wsi18, a stress-inducible promoter that is active in the whole grain of transgenic rice. Transgenic Res. 2011 Feb;20(1):153–63. PubMed Europe PMC Scholia" -20567981 Pubmed "Yi N, Kim YS, Jeong M-H, Oh S-J, Jeong JS, Park S-H, et al. Functional analysis of six drought-inducible promoters in transgenic rice plants throughout all stages of plant growth. Planta. 2010 Aug;232(3):743–54. PubMed Europe PMC Scholia" -20632034 Pubmed "Takasaki H, Maruyama K, Kidokoro S, Ito Y, Fujita Y, Shinozaki K, et al. The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Mol Genet Genomics. 2010 Sep;284(3):173–83. PubMed Europe PMC Scholia" -20713616 Pubmed "Fu F-F, Xue H-W. Coexpression analysis identifies Rice Starch Regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator. Plant Physiol. 2010 Oct;154(2):927–38. PubMed Europe PMC Scholia" -20829346 Pubmed "Yu G, Olsen KM, Schaal BA. Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L. Mol Biol Evol. 2011 Jan;28(1):659–71. PubMed Europe PMC Scholia" -20889913 Pubmed "She K-C, Kusano H, Koizumi K, Yamakawa H, Hakata M, Imamura T, et al. A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. Plant Cell. 2010 Oct;22(10):3280–94. PubMed Europe PMC Scholia" -20974950 Pubmed "Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, et al. Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19579–84. PubMed Europe PMC Scholia" -21037241 Pubmed "Kawakatsu T, Takaiwa F. Differences in transcriptional regulatory mechanisms functioning for free lysine content and seed storage protein accumulation in rice grain. Plant Cell Physiol. 2010 Dec;51(12):1964–74. PubMed Europe PMC Scholia" -24280312 Pubmed "Hanumappa M, Preece J, Elser J, Nemeth D, Bono G, Wu K, et al. WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. Rice (N Y). 2013 May 29;6(1):14. PubMed Europe PMC Scholia" +8193305 Pubmed "Sequence and functional analyses of the rice gene homologous to the maize Vp1. Hattori T, Terada T, Hamasuna ST. Plant Mol Biol. 1994 Mar;24(5):805–10. PubMed Europe PMC Scholia" +8940135 Pubmed "Characterization of three rice basic/leucine zipper factors, including two inhibitors of EmBP-1 DNA binding activity. Nantel A, Quatrano RS. J Biol Chem. 1996 Dec 6;271(49):31296–305. PubMed Europe PMC Scholia" +9596641 Pubmed "14-3-3 proteins are part of an abscisic acid-VIVIPAROUS1 (VP1) response complex in the Em promoter and interact with VP1 and EmBP1. Schultz TF, Medina J, Hill A, Quatrano RS. Plant Cell. 1998 May;10(5):837–47. PubMed Europe PMC Scholia" +10417713 Pubmed "RNA maturation of the rice SPK gene may involve trans-splicing. Kawasaki T, Okumura S, Kishimoto N, Shimada H, Higo K, Ichikawa N. Plant J. 1999 Jun;18(6):625–32. PubMed Europe PMC Scholia" +10805599 Pubmed "Hormonal cross-talk between auxin and ethylene differentially regulates the expression of two members of the 1-aminocyclopropane-1-carboxylate oxidase gene family in rice (Oryza sativa L.). Chae HS, Cho YG, Park MY, Lee MC, Eun MY, Kang BG, et al. Plant Cell Physiol. 2000 Mar;41(3):354–62. PubMed Europe PMC Scholia" +10987556 Pubmed "The cell cycle genes cycA1;1 and cdc2Os-3 are coordinately regulated by gibberellin in planta. Fabian T, Lorbiecke R, Umeda M, Sauter M. Planta. 2000 Aug;211(3):376–83. PubMed Europe PMC Scholia" +11910009 Pubmed "Rice SPK, a calmodulin-like domain protein kinase, is required for storage product accumulation during seed development: phosphorylation of sucrose synthase is a possible factor. Asano T, Kunieda N, Omura Y, Ibe H, Kawasaki T, Takano M, et al. Plant Cell. 2002 Mar;14(3):619–28. PubMed Europe PMC Scholia" +12684538 Pubmed "A network of rice genes associated with stress response and seed development. Cooper B, Clarke JD, Budworth P, Kreps J, Hutchison D, Park S, et al. Proc Natl Acad Sci U S A. 2003 Apr 15;100(8):4945–50. PubMed Europe PMC Scholia" +12783325 Pubmed "Interaction between proliferating cell nuclear antigen and JUN-activation-domain-binding protein 1 in the meristem of rice, Oryza sativa L. Yamamoto T, Kimura S, Mori Y, Uchiyama Y, Ishibashi T, Hashimoto J, et al. Planta. 2003 Jun;217(2):175–83. PubMed Europe PMC Scholia" +12947109 Pubmed "An interaction between a MYC protein and an EREBP protein is involved in transcriptional regulation of the rice Wx gene. Zhu Y, Cai XL, Wang ZY, Hong MM. J Biol Chem. 2003 Nov 28;278(48):47803–11. PubMed Europe PMC Scholia" +14733924 Pubmed "Characterization of Rad6 from a higher plant, rice (Oryza sativa L.) and its interaction with Sgt1, a subunit of the SCF ubiquitin ligase complex. Yamamoto T, Mori Y, Ishibashi T, Uchiyama Y, Sakaguchi N, Furukawa T, et al. Biochem Biophys Res Commun. 2004 Feb 6;314(2):434–9. PubMed Europe PMC Scholia" +15047897 Pubmed "A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. Zhang ZL, Xie Z, Zou X, Casaretto J, Ho THD, Shen QJ. Plant Physiol. 2004 Apr;134(4):1500–13. PubMed Europe PMC Scholia" +15220467 Pubmed "Down-regulation of metallothionein, a reactive oxygen scavenger, by the small GTPase OsRac1 in rice. Wong HL, Sakamoto T, Kawasaki T, Umemura K, Shimamoto K. Plant Physiol. 2004 Jul;135(3):1447–56. PubMed Europe PMC Scholia" +15232694 Pubmed "A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). Hirose T, Terao T. Planta. 2004 Nov;220(1):9–16. PubMed Europe PMC Scholia" +15356337 Pubmed "A rice antisense SPK transformant that lacks the accumulation of seed storage substances shows no correlation between sucrose concentration in phloem sap and demand for carbon sources in the sink organs. Shimada H, Koishihara H, Saito Y, Arashima Y, Furukawa T, Hayashi H. Plant Cell Physiol. 2004 Aug;45(8):1105–9. PubMed Europe PMC Scholia" +15759120 Pubmed "Molecular cloning and expression analysis of the cell-wall invertase gene family in rice (Oryza sativa L.). Cho JI, Lee SK, Ko S, Kim HK, Jun SH, Lee YH, et al. Plant Cell Rep. 2005 Jun;24(4):225–36. PubMed Europe PMC Scholia" +15806324 Pubmed "Interaction between proliferating cell nuclear antigen (PCNA) and a DnaJ induced by DNA damage. Yamamoto T, Mori Y, Ishibashi T, Uchiyama Y, Ueda T, Ando T, et al. J Plant Res. 2005 Apr;118(2):91–7. PubMed Europe PMC Scholia" +15891897 Pubmed "Identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins. Kasai K, Kanno T, Akita M, Ikejiri-Kanno Y, Wakasa K, Tozawa Y. Planta. 2005 Oct;222(3):438–47. PubMed Europe PMC Scholia" +15976269 Pubmed "Cytokinin oxidase regulates rice grain production. Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, et al. Science. 2005 Jul 29;309(5735):741–5. PubMed Europe PMC Scholia" +16152656 Pubmed "Proteomic analysis of rice embryo: an approach for investigating Galpha protein-regulated proteins. Komatsu S, Abbasi F, Kobori E, Fujisawa Y, Kato H, Iwasaki Y. Proteomics. 2005 Oct;5(15):3932–41. PubMed Europe PMC Scholia" +16275672 Pubmed "Expression profiling of genes involved in starch synthesis in sink and source organs of rice. Ohdan T, Francisco PB Jr, Sawada T, Hirose T, Terao T, Satoh H, et al. J Exp Bot. 2005 Dec;56(422):3229–44. PubMed Europe PMC Scholia" +16436304 Pubmed "Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress. Cao Y, Song F, Goodman RM, Zheng Z. J Plant Physiol. 2006 Nov;163(11):1167–78. PubMed Europe PMC Scholia" +16623886 Pubmed "Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. Xie Z, Zhang ZL, Zou X, Yang G, Komatsu S, Shen QJ. Plant J. 2006 Apr;46(2):231–42. PubMed Europe PMC Scholia" +16667159 Pubmed "Effects of cold-treatment on protein synthesis and mRNA levels in rice leaves. Hahn M, Walbot V. Plant Physiol. 1989 Nov;91(3):930–8. PubMed Europe PMC Scholia" +16786297 Pubmed "OsEIL1, a rice homolog of the Arabidopsis EIN3 regulates the ethylene response as a positive component. Mao C, Wang S, Jia Q, Wu P. Plant Mol Biol. 2006 May;61(1–2):141–52. PubMed Europe PMC Scholia" +16798940 Pubmed "Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes. Yamamoto MP, Onodera Y, Touno SM, Takaiwa F. Plant Physiol. 2006 Aug;141(4):1694–707. PubMed Europe PMC Scholia" +16896230 Pubmed "Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. Li X, Duan X, Jiang H, Sun Y, Tang Y, Yuan Z, et al. Plant Physiol. 2006 Aug;141(4):1167–84. PubMed Europe PMC Scholia" +16953433 Pubmed "Structural and enzymatic characterization of the isoamylase1 homo-oligomer and the isoamylase1-isoamylase2 hetero-oligomer from rice endosperm. Utsumi Y, Nakamura Y. Planta. 2006 Dec;225(1):75–87. PubMed Europe PMC Scholia" +17297616 Pubmed "Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.). Ryoo N, Yu C, Park CS, Baik MY, Park IM, Cho MH, et al. Plant Cell Rep. 2007 Jul;26(7):1083–95. PubMed Europe PMC Scholia" +17339651 Pubmed "OsMTN encodes a 5’-methylthioadenosine nucleosidase that is up-regulated during submergence-induced ethylene synthesis in rice (Oryza sativa L.). Rzewuski G, Cornell KA, Rooney L, Bürstenbinder K, Wirtz M, Hell R, et al. J Exp Bot. 2007;58(6):1505–14. PubMed Europe PMC Scholia" +17376611 Pubmed "Characterization of a lipoate-protein ligase A gene of rice (Oryza sativa L.). Kang SG, Jeong HK, Lee E, Natarajan S. Gene. 2007 May 15;393(1–2):53–61. PubMed Europe PMC Scholia" +17384160 Pubmed "Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. Yamakawa H, Hirose T, Kuroda M, Yamaguchi T. Plant Physiol. 2007 May;144(1):258–77. PubMed Europe PMC Scholia" +17406793 Pubmed "Identification of the ADP-glucose pyrophosphorylase isoforms essential for starch synthesis in the leaf and seed endosperm of rice (Oryza sativa L.). Lee SK, Hwang SK, Han M, Eom JS, Kang HG, Han Y, et al. Plant Mol Biol. 2007 Nov;65(4):531–46. PubMed Europe PMC Scholia" +17426956 Pubmed "Over-expression of a LEA gene in rice improves drought resistance under the field conditions. Xiao B, Huang Y, Tang N, Xiong L. Theor Appl Genet. 2007 Jun;115(1):35–46. PubMed Europe PMC Scholia" +17559517 Pubmed "The rice bHLH protein OsIRO2 is an essential regulator of the genes involved in Fe uptake under Fe-deficient conditions. Ogo Y, Itai RN, Nakanishi H, Kobayashi T, Takahashi M, Mori S, et al. Plant J. 2007 Aug;51(3):366–77. PubMed Europe PMC Scholia" +17579813 Pubmed "Du1, encoding a novel Prp1 protein, regulates starch biosynthesis through affecting the splicing of Wxb pre-mRNAs in rice (Oryza sativa L.). Zeng D, Yan M, Wang Y, Liu X, Qian Q, Li J. Plant Mol Biol. 2007 Nov;65(4):501–9. PubMed Europe PMC Scholia" +17587305 Pubmed "Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. Nakashima K, Tran LSP, Van Nguyen D, Fujita M, Maruyama K, Todaka D, et al. Plant J. 2007 Aug;51(4):617–30. PubMed Europe PMC Scholia" +17604002 Pubmed "Characterization of alternative splicing products of bZIP transcription factors OsABI5. Zou M, Guan Y, Ren H, Zhang F, Chen F. Biochem Biophys Res Commun. 2007 Aug 24;360(2):307–13. PubMed Europe PMC Scholia" +17640358 Pubmed "MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. Arora R, Agarwal P, Ray S, Singh AK, Singh VP, Tyagi AK, et al. BMC Genomics. 2007 Jul 18;8:242. PubMed Europe PMC Scholia" +18025467 Pubmed "The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants. Kobayashi T, Ogo Y, Itai RN, Nakanishi H, Takahashi M, Mori S, et al. Proc Natl Acad Sci U S A. 2007 Nov 27;104(48):19150–5. PubMed Europe PMC Scholia" +18156216 Pubmed "RAR1 and HSP90 form a complex with Rac/Rop GTPase and function in innate-immune responses in rice. Thao NP, Chen L, Nakashima A, Hara S ichiro, Umemura K, Takahashi A, et al. Plant Cell. 2007 Dec;19(12):4035–45. PubMed Europe PMC Scholia" +18257679 Pubmed "OsRAR1 and OsSGT1 physically interact and function in rice basal disease resistance. Wang Y, Gao M, Li Q, Wang L, Wang J, Jeon JS, et al. Mol Plant Microbe Interact. 2008 Mar;21(3):294–303. PubMed Europe PMC Scholia" +18308732 Pubmed "A novel NAC transcription factor, IDEF2, that recognizes the iron deficiency-responsive element 2 regulates the genes involved in iron homeostasis in plants. Ogo Y, Kobayashi T, Nakanishi Itai R, Nakanishi H, Kakei Y, Takahashi M, et al. J Biol Chem. 2008 May 9;283(19):13407–17. PubMed Europe PMC Scholia" +18315698 Pubmed "Abscisic acid regulates gene expression in cortical fiber cells and silica cells of rice shoots. Shobbar ZS, Oane R, Gamuyao R, De Palma J, Malboobi MA, Karimzadeh G, et al. New Phytol. 2008;178(1):68–79. PubMed Europe PMC Scholia" +18454147 Pubmed "Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice. Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, et al. Nat Genet. 2008 Jun;40(6):761–7. PubMed Europe PMC Scholia" +18599581 Pubmed "Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. Chen S, Yang Y, Shi W, Ji Q, He F, Zhang Z, et al. Plant Cell. 2008 Jul;20(7):1850–61. PubMed Europe PMC Scholia" +18713381 Pubmed "Cell-wall invertases from rice are differentially expressed in Caryopsis during the grain filling stage. Wang YQ, Wei XL, Xu HL, Chai CL, Meng K, Zhai HL, et al. J Integr Plant Biol. 2008 Apr;50(4):466–74. PubMed Europe PMC Scholia" +18723578 Pubmed "RACK1 functions in rice innate immunity by interacting with the Rac1 immune complex. Nakashima A, Chen L, Thao NP, Fujiwara M, Wong HL, Kuwano M, et al. Plant Cell. 2008 Aug;20(8):2265–79. PubMed Europe PMC Scholia" +18755073 Pubmed "Identification and characterization of a rice MCM2 homologue required for DNA replication. Cho JH, Kim HB, Kim HS, Choi SB. BMB Rep. 2008 Aug 31;41(8):581–6. PubMed Europe PMC Scholia" +18820698 Pubmed "Control of rice grain-filling and yield by a gene with a potential signature of domestication. Wang E, Wang J, Zhu X, Hao W, Wang L, Li Q, et al. Nat Genet. 2008 Nov;40(11):1370–4. PubMed Europe PMC Scholia" +18826428 Pubmed "Contribution of salicylic acid glucosyltransferase, OsSGT1, to chemically induced disease resistance in rice plants. Umemura K, Satou J, Iwata M, Uozumi N, Koga J, Kawano T, et al. Plant J. 2009 Feb;57(3):463–72. PubMed Europe PMC Scholia" +18840300 Pubmed "RNAi-directed downregulation of OsBADH2 results in aroma (2-acetyl-1-pyrroline) production in rice (Oryza sativa L.). Niu X, Tang W, Huang W, Ren G, Wang Q, Luo D, et al. BMC Plant Biol. 2008 Oct 8;8:100. PubMed Europe PMC Scholia" +19015668 Pubmed "Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Weng J, Gu S, Wan X, Gao H, Guo T, Su N, et al. Cell Res. 2008 Dec;18(12):1199–209. PubMed Europe PMC Scholia" +19052152 Pubmed "Rice aldehyde dehydrogenase7 is needed for seed maturation and viability. Shin JH, Kim SR, An G. Plant Physiol. 2009 Feb;149(2):905–15. PubMed Europe PMC Scholia" +19266169 Pubmed "Characterization of OsIAA1 gene, a member of rice Aux/IAA family involved in auxin and brassinosteroid hormone responses and plant morphogenesis. Song Y, You J, Xiong L. Plant Mol Biol. 2009 Jun;70(3):297–309. PubMed Europe PMC Scholia" +19321714 Pubmed "Spatiotemporal profiling of starch biosynthesis and degradation in the developing barley grain. Radchuk VV, Borisjuk L, Sreenivasulu N, Merx K, Mock HP, Rolletschek H, et al. Plant Physiol. 2009 May;150(1):190–204. PubMed Europe PMC Scholia" +19429605 Pubmed "Overexpression of the transcription factor AP37 in rice improves grain yield under drought conditions. Oh SJ, Kim YS, Kwon CW, Park HK, Jeong JS, Kim JK. Plant Physiol. 2009 Jul;150(3):1368–79. PubMed Europe PMC Scholia" +19473328 Pubmed "Compensation and interaction between RISBZ1 and RPBF during grain filling in rice. Kawakatsu T, Yamamoto MP, Touno SM, Yasuda H, Takaiwa F. Plant J. 2009 Sep;59(6):908–20. PubMed Europe PMC Scholia" +19490115 Pubmed "Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. Jain M, Khurana JP. FEBS J. 2009 Jun;276(11):3148–62. PubMed Europe PMC Scholia" +19506305 Pubmed "Evolutionary history of GS3, a gene conferring grain length in rice. Takano-Kai N, Jiang H, Kubo T, Sweeney M, Matsumoto T, Kanamori H, et al. Genetics. 2009 Aug;182(4):1323–34. PubMed Europe PMC Scholia" +19593540 Pubmed "Comparison of the starch synthesis genes between maize and rice: copies, chromosome location and expression divergence. Yan HB, Pan XX, Jiang HW, Wu GJ. Theor Appl Genet. 2009 Sep;119(5):815–25. PubMed Europe PMC Scholia" +19682292 Pubmed "Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling. Bi YM, Kant S, Clarke J, Gidda S, Ming F, Xu J, et al. Plant Cell Environ. 2009 Dec;32(12):1749–60. PubMed Europe PMC Scholia" +19737364 Pubmed "The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes. Kobayashi T, Itai RN, Ogo Y, Kakei Y, Nakanishi H, Takahashi M, et al. Plant J. 2009 Dec;60(6):948–61. PubMed Europe PMC Scholia" +19807881 Pubmed "Inactivation of the CTD phosphatase-like gene OsCPL1 enhances the development of the abscission layer and seed shattering in rice. Ji H, Kim SR, Kim YH, Kim H, Eun MY, Jin ID, et al. Plant J. 2010 Jan;61(1):96–106. PubMed Europe PMC Scholia" +19921249 Pubmed "The expression of Orysa;CycB1;1 is essential for endosperm formation and causes embryo enlargement in rice. Guo J, Wang F, Song J, Sun W, Zhang XS. Planta. 2010 Jan;231(2):293–303. PubMed Europe PMC Scholia" +19933315 Pubmed "The syncytium-specific expression of the Orysa;KRP3 CDK inhibitor: implication of its involvement in the cell cycle control in the rice (Oryza sativa L.) syncytial endosperm. Mizutani M, Naganuma T, Tsutsumi K ichi, Saitoh Y. J Exp Bot. 2010 Mar;61(3):791–8. PubMed Europe PMC Scholia" +20220098 Pubmed "Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. Sugimoto K, Takeuchi Y, Ebana K, Miyao A, Hirochika H, Hara N, et al. Proc Natl Acad Sci U S A. 2010 Mar 30;107(13):5792–7. PubMed Europe PMC Scholia" +20305271 Pubmed "Characterization of the reactions of starch branching enzymes from rice endosperm. Nakamura Y, Utsumi Y, Sawada T, Aihara S, Utsumi C, Yoshida M, et al. Plant Cell Physiol. 2010 May;51(5):776–94. PubMed Europe PMC Scholia" +20335401 Pubmed "Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Jeong JS, Kim YS, Baek KH, Jung H, Ha SH, Do Choi Y, et al. Plant Physiol. 2010 May;153(1):185–97. PubMed Europe PMC Scholia" +20416079 Pubmed "Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication. Wang E, Xu X, Zhang L, Zhang H, Lin L, Wang Q, et al. BMC Evol Biol. 2010 Apr 23;10:108. PubMed Europe PMC Scholia" +20460361 Pubmed "Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice. Sun SJ, Guo SQ, Yang X, Bao YM, Tang HJ, Sun H, et al. J Exp Bot. 2010 Jun;61(10):2807–18. PubMed Europe PMC Scholia" +20478538 Pubmed "Activation of a Rac GTPase by the NLR family disease resistance protein Pit plays a critical role in rice innate immunity. Kawano Y, Akamatsu A, Hayashi K, Housen Y, Okuda J, Yao A, et al. Cell Host Microbe. 2010 May 20;7(5):362–75. PubMed Europe PMC Scholia" +20490919 Pubmed "Analysis of the Wsi18, a stress-inducible promoter that is active in the whole grain of transgenic rice. Yi N, Oh SJ, Kim YS, Jang HJ, Park SH, Jeong JS, et al. Transgenic Res. 2011 Feb;20(1):153–63. PubMed Europe PMC Scholia" +20567981 Pubmed "Functional analysis of six drought-inducible promoters in transgenic rice plants throughout all stages of plant growth. Yi N, Kim YS, Jeong MH, Oh SJ, Jeong JS, Park SH, et al. Planta. 2010 Aug;232(3):743–54. PubMed Europe PMC Scholia" +20632034 Pubmed "The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. Takasaki H, Maruyama K, Kidokoro S, Ito Y, Fujita Y, Shinozaki K, et al. Mol Genet Genomics. 2010 Sep;284(3):173–83. PubMed Europe PMC Scholia" +20713616 Pubmed "Coexpression analysis identifies Rice Starch Regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator. Fu FF, Xue HW. Plant Physiol. 2010 Oct;154(2):927–38. PubMed Europe PMC Scholia" +20829346 Pubmed "Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L. Yu G, Olsen KM, Schaal BA. Mol Biol Evol. 2011 Jan;28(1):659–71. PubMed Europe PMC Scholia" +20889913 Pubmed "A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. She KC, Kusano H, Koizumi K, Yamakawa H, Hakata M, Imamura T, et al. Plant Cell. 2010 Oct;22(10):3280–94. PubMed Europe PMC Scholia" +20974950 Pubmed "Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, et al. Proc Natl Acad Sci U S A. 2010 Nov 9;107(45):19579–84. PubMed Europe PMC Scholia" +21037241 Pubmed "Differences in transcriptional regulatory mechanisms functioning for free lysine content and seed storage protein accumulation in rice grain. Kawakatsu T, Takaiwa F. Plant Cell Physiol. 2010 Dec;51(12):1964–74. PubMed Europe PMC Scholia" +24280312 Pubmed "WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks. Hanumappa M, Preece J, Elser J, Nemeth D, Bono G, Wu K, et al. Rice (N Y). 2013 May 29;6(1):14. PubMed Europe PMC Scholia" diff --git a/pathways/WP2199/WP2199-datanodes.tsv b/pathways/WP2199/WP2199-datanodes.tsv index dbf65b10b..8096bd58d 100644 --- a/pathways/WP2199/WP2199-datanodes.tsv +++ b/pathways/WP2199/WP2199-datanodes.tsv @@ -1,434 +1,433 @@ -Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI -HOX 22 GeneProduct :LOC_Os04g45810 In Cooper et al. 2003 protein sequence provided matches HOX 22, however it was named HOX6 (AF145730) -Dynamin GeneProduct :LOC_Os06g13820 -IAA amidohydrolase GeneProduct :LOC_Os03g62060 -HSP40 GeneProduct :LOC_Os03g44620 -bHLH60 GeneProduct :LOC_Os08g04390 Helix-loop-helix TF -MADS 18 GeneProduct :LOC_Os07g41370 Also called MADS 28 -PPDKB GeneProduct :LOC_Os05g33570 Involved in grain filling -2-d-3-D phosphooctonate aldolase GeneProduct :LOC_Os12g10784 -GB2 GeneProduct :LOC_Os03g57960 Globulin 2 -BTB/POZ GeneProduct :LOC_Os10g29390 2-keto-3-deoxy-6-phosphogluconate aldolase -LOC_Os06g39906 GeneProduct :LOC_Os06g39906 -NB-ARC domain protein GeneProduct :LOC_Os11g34880 Jacalin -ZF-like GeneProduct :LOC_Os01g40990 -grpA3 GeneProduct :LOC_Os05g02780 -EXPB4 GeneProduct :LOC_Os10g40730 Beta-expansin-4 -Bam 4 GeneProduct :LOC_Os07g47120 -Pyrrolidone-Carboxylpeptidase GeneProduct :LOC_Os03g25270 -SPS-O spp GeneProduct :LOC_Os08g20660 sucrose-phosphate synthase-Oncidium spp= named after table III on Yamakawa et al. (2007) -IAA4 GeneProduct :LOC_Os01g18360 -Cyp2 GeneProduct :LOC_Os02g02890 -Bam 7 GeneProduct :LOC_Os03g04770 -Thioredoxin-like GeneProduct :LOC_Os04g57310 thiol-disulphide oxidoreductase DCC -Shaggy kinase GeneProduct :LOC_Os10g37740 -Pto kinase Interactor 1 GeneProduct :LOC_Os05g04520 -LOC_Os09g38090 GeneProduct :LOC_Os09g38090 -PCNA GeneProduct :LOC_Os02g56130 Proliferating cell nuclear antigen expressed strongly in the shoot apical meristem -GDSL-like Lipase GeneProduct :LOC_Os10g05088 SGNH_plant_lipase -PP2A-3 GeneProduct :LOC_Os02g12580 -TRNA endonuclease GeneProduct :LOC_Os11g38930 catalytic C-terminal domain containing protein -SSIVb GeneProduct :LOC_Os05g45720 Also called ALK -UDP-glucosyl transferase GeneProduct :LOC_Os04g12960 -WRKY 51 GeneProduct :LOC_Os04g21950 ABA-inducible & GA-repressible WRKY 51 by itself also represses activation of Amy2A by GAMYB -RSR1 GeneProduct :LOC_Os01g40280 -RAD6 GeneProduct :LOC_Os03g57790 transcripts of both OsRad6 and OsSgt1 were found to be strongly expressed in the proliferating tissues such SAM -HAD-like GeneProduct :LOC_Os03g16670 -Myosin like GeneProduct :LOC_Os05g02820 -SAM cmtr GeneProduct :LOC_Os02g06770 -Kinesin GeneProduct :LOC_Os03g43100 -SSIIIb GeneProduct :LOC_Os04g53310 Also called ALK - EF-1-d2 GeneProduct :LOC_Os03g29260 Elongation factor 1 beta 2 -Keto acyl CoA thiolase GeneProduct :LOC_Os02g57260 -OsFBX237 GeneProduct :LOC_Os07g35050 Cdc2-related protein kinase -ZIP-1a GeneProduct :LOC_Os12g13170 -eif(iso)4g GeneProduct :LOC_Os04g42140 -Fructose-6-phosphate 1-phosphotransferase GeneProduct :LOC_Os08g25720 -GluA-3 GeneProduct :LOC_Os03g31360 -RAV1-like GeneProduct :LOC_Os01g49830 -LEA 14-A GeneProduct :LOC_Os05g50710 -GABA permease GeneProduct :LOC_Os01g71720 Amino acid/polyamine transporter -OsIAA13 GeneProduct :LOC_Os03g53150 -OSE2 GeneProduct :LOC_Os01g64730 bZIP transcription factor domain containing protein -MAPK2 GeneProduct :LOC_Os02g05480 UniProt:MAPK2, BIMK1, MAP3, MAPK5, MPK3, MSRMK2 -IDI2 GeneProduct :LOC_Os11g11050 Initiation factor 2 subunit family protein -AP37 GeneProduct :LOC_Os01g58420 -SNAC1 GeneProduct :LOC_Os03g60080 -IDS1/ MT4A GeneProduct :LOC_Os12g38270 -GBSSII GeneProduct :LOC_Os07g22930 Also called ALK -Ser/thr PK GeneProduct :LOC_Os06g04880 -LOC_Os03g50390 GeneProduct :LOC_Os03g50390 Protein Kinase-UniProt ID -PRP1 GeneProduct :LOC_Os05g13940 -INV2 GeneProduct :LOC_Os01g22900 Neutral/alkaline invertase 2 Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010) -Phosphoglucomutase GeneProduct :LOC_Os05g48200 - EPSPS1 GeneProduct :LOC_Os06g04280 5-Enolpyruvylshikimate-3-phosphate synthase 1 -APL4/ AGPL4 GeneProduct :LOC_Os07g13980 -CycD2-2 GeneProduct :LOC_Os07g42860 -Amy3A GeneProduct :LOC_Os09g28400 -TPR-PK GeneProduct :LOC_Os03g61010 Putative protein kinase -SPS-Zm GeneProduct :LOC_Os06g42824 sucrose-phosphate synthase-Zea mays= named after table III on Yamakawa et al. (2007) -FERTILLIN GeneProduct :LOC_Os06g01650 -Disease resistance-like GeneProduct :LOC_Os12g40490 LIM domain-containing protein, putative, expressed -bip129 GeneProduct :LOC_Os08g40790 -KOB1 GeneProduct :LOC_Os02g57240 Probable voltage-gated potassium channel subunit beta -GP-alpha-1 GeneProduct :LOC_Os05g26890 G-alpha protein also called GPA1/D1/GA1 -DAHPS1 GeneProduct :LOC_Os03g27230 3-deoxy-D-arabino heptulosonate-7-phosphate synthase 1 -NAAT1 GeneProduct :LOC_Os02g20360 nicotianamine aminotransferase -NAC5 GeneProduct :LOC_Os11g08210 ABA related -SSIIIa/ Flo5 GeneProduct :LOC_Os08g09230 expression diminished during grain filling at high temperatures -Amy4A GeneProduct :LOC_Os01g51754 -NAC2 GeneProduct :LOC_Os02g57650 -U2 snRNP GeneProduct :LOC_Os11g41820 -SPS-So GeneProduct :LOC_Os06g43630 sucrose-phosphate synthase-Saccharum officinarum= named after table III on Yamakawa et al. (2007) -Pr1b GeneProduct :LOC_Os01g28450 -GluA-2 GeneProduct :LOC_Os10g26060 -MTN GeneProduct :LOC_Os06g02220 Methylthioadenosine/S-adenosyl homocysteine nucleosidase -RPS20 GeneProduct :LOC_Os06g04290 P35686 -Phosphotyrosine GeneProduct :LOC_Os08g44320 -Ser/thr PK GeneProduct :LOC_Os02g43290 -ZOS1-15 GeneProduct :LOC_Os01g62190 Salt-stress ABA related -MADS7/45 GeneProduct :LOC_Os08g41950 also called MADS 45, AGL6, M79 -ARD2 GeneProduct :LOC_Os03g06620 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 2; Also called IDI1 and SIP2A -GAMYB GeneProduct :LOC_Os01g59660 regulates GA induction of Amy2A -ALDH7 GeneProduct :LOC_Os09g26880 Needed for seed maturation and viability. Expression Patterns during Seed Development Correspond with Pigment Accumulation Patterns in Seeds Plays a role in the removal of MDA that forms during seed desiccation -DOF ZF GeneProduct :LOC_Os02g49440 -WRKY 71 GeneProduct :LOC_Os02g08440 ABA-inducible & GA-repressible Interaction between WRKY 51 and 71 enhances the binding affinity of WRKY71 to the Amy32b promoter WRKY 71 by itself also represses activation of Amy2A by GAMYB -Complex 1L GeneProduct :LOC_Os06g50000 Assigned as Complex 1L by Nemeth D and Hanumappa M (10/21/2010) complex 1 family protein-like (LYR family) -PP2A-B GeneProduct :LOC_Os05g40350 -GF14A GeneProduct :LOC_Os08g37490 WIN2, WIP2 -PROLM26 GeneProduct :LOC_Os07g10580 Prolamin precursor, also called RP5 -MT2b GeneProduct :LOC_Os05g02070 -IAA1 GeneProduct :LOC_Os01g08320 -LOC_Os01g14110 GeneProduct :LOC_Os01g14110 Assigned as bHLH-tf by Nemeth D and Hanumappa M (10/21/2010) -TAP46 GeneProduct :LOC_Os12g04290 -PIT GeneProduct :LOC_Os01g05620 -Permease GeneProduct :LOC_Os07g04180 -SSII-3 GeneProduct :LOC_Os06g12450 expression diminished during grain filling at high temperatures -SuSy6 GeneProduct :LOC_Os04g24430 Sucrose synthase 6 -NAC 10 GeneProduct :LOC_Os11g03300 -Myosin like GeneProduct :LOC_Os03g16120 -Sub9 GeneProduct :LOC_Os01g58290 Amino acid transporters -DUF630 GeneProduct :LOC_Os10g41310 Symbol assigned by Nemeth D and Hanumappa M (08/19/2010) -CACTA, En/Spm GeneProduct :LOC_Os01g09220 -CDKA-2 GeneProduct :LOC_Os02g03060 -PHT4;3 GeneProduct :LOC_Os01g63290 Na+ dep inorg phosphate cotransporter -Oryzain alpha Protease GeneProduct :LOC_Os04g55650 -msrB-1 GeneProduct :LOC_Os03g24600 2 more IDs found on Gramene. Hence called 1, 2 and 3 to differentiate. LOC_Os06g27760=msrB-2, LOC_Os05g33510=msrB-3 (D Nemeth and M Hanumappa 08/17/2010).
Type your comment here -GTP cyclohydrolase GeneProduct :LOC_Os05g38570 GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate synthase -Ubiquitin proteinase GeneProduct :LOC_Os02g43760 ubiquitin carboxyl-terminal hydrolase, family 1, putative, expressed -PP2A1 GeneProduct :LOC_Os06g37660 -LOC_Os01g62740 GeneProduct :LOC_Os01g62740 -Bam 5 GeneProduct :LOC_Os10g32810 -AP2 domain GeneProduct :LOC_Os03g64260 -SET domain protein GeneProduct :LOC_Os02g40770 histone-lysine N-methyltransferase -UOS1 GeneProduct :LOC_Os06g49120 NAD(P)-binding/Rossman fold -SPK GeneProduct :LOC_Os10g39420 required for storage product accumulation during seed development seed-specific protein kinase -MADS 3 GeneProduct :LOC_Os01g10504 Also called RAG -USP1 GeneProduct :LOC_Os07g47620 ETFP adenine nucleotide -LOC_Os03g56940 GeneProduct :LOC_Os03g56940 -GPT2-B GeneProduct :LOC_Os01g07310 Assigned as GPT-B by Nemeth D and Hanumappa M (10/21/2010) -BT1-1 GeneProduct :LOC_Os05g07900 -SPS-Hv GeneProduct :LOC_Os02g09170 sucrose-phosphate synthase-Hordeum vulgare= named after table III on Yamakawa et al. (2007) -LPLA GeneProduct :LOC_Os08g33810 -NAS2 GeneProduct :LOC_Os03g19420 NA synthase gene 2 -GW2 GeneProduct :LOC_Os02g14720 encodes a RING protein with E3 ubiquitin ligase activity -GDSL-like Lipase GeneProduct :LOC_Os01g11650 -ARF1 GeneProduct :LOC_Os11g32110 -UGP GeneProduct :LOC_Os02g02550 -DEP GeneProduct :LOC_Os11g29370 Haloacid dehalogenase-like hydrolase family protein -flavanone 3-hydroxylase GeneProduct :LOC_Os08g37456 2-oxoglutarate (2OG) - Fe(II) oxygenase -BBTI4 GeneProduct :LOC_Os01g03340 Bowman-Birk type bran trypsin inhibitor -HMG1 GeneProduct :LOC_Os06g51220 -PPROL 14 E GeneProduct :LOC_Os05g26377 13 kDa Prolamin, also called PPROL 14, PPROL 4A, PPROL 7, PG5a, PROLM 8, PROLM 9, UniProt ID: Q95737 -CIN1 GeneProduct :LOC_Os02g33110 -ADP ribosylation GTPase GeneProduct :LOC_Os03g17020 -MADS 6 GeneProduct :LOC_Os02g45770 Also called MFO1 -GLUB4 GeneProduct :LOC_Os02g16830 -SuSy4 GeneProduct :LOC_Os03g22120 Sucrose synthase 4 -GF14-e GeneProduct :LOC_Os02g36974 -CDKA-1 GeneProduct :LOC_Os03g02680 -IDEF2 GeneProduct :LOC_Os05g35170 IDE-binding factor 2 -SUS1 GeneProduct :LOC_Os03g28330 Sucrose synthase 1 -LOC_Os01g12080 GeneProduct :LOC_Os01g12080 -Amy3E GeneProduct :LOC_Os08g36900 -prx61 GeneProduct :LOC_Os04g59190 Class III peroxidase 61 -MADS13 GeneProduct :LOC_Os12g10540 Also called MAF1 -SWEET3a GeneProduct :LOC_Os05g12320 -BEIII GeneProduct :LOC_Os06g26234 -Pectinesterase GeneProduct :LOC_Os07g02810 -VIP1-like GeneProduct :LOC_Os06g02240 -AREB GeneProduct :LOC_Os05g41070 -PPDKA GeneProduct :LOC_Os03g31750 Assigned as GPT-B by Nemeth D and Hanumappa M (10/21/2010) -PUL GeneProduct :LOC_Os04g08270 expression diminished during grain filling at high temperatures -CCT/B-box zinc finger GeneProduct :LOC_Os02g49230 -CIN3 GeneProduct :LOC_Os04g33720 -TUBB3 GeneProduct :LOC_Os06g46000 Tubulin beta-3 chain -ACO1 GeneProduct :LOC_Os09g27750 -SAP11 GeneProduct :LOC_Os08g39450 Also called ZFP60 -MADS47 GeneProduct :LOC_Os03g08754 Also called MDP -KRP3 GeneProduct :LOC_Os11g40030 -DMAS1 GeneProduct :LOC_Os03g13390 Deoxymugineic acid synthase1 -CIN5 GeneProduct :LOC_Os04g56930 -LOC_Os03g07360 GeneProduct :LOC_Os03g07360 -RIC1 GeneProduct :LOC_Os01g37800 -RBCL GeneProduct :LOC_Os10g21268 -CIN2 GeneProduct :LOC_Os04g33740 -DEK1 GeneProduct :LOC_Os02g48000 -RA GeneProduct :LOC_Os04g47080 seed coat color, endosperm color -HSP90 GeneProduct :LOC_Os09g30418 Also called HSP81-2 -GF14F GeneProduct :LOC_Os03g50290 G-box factor 14-3-3 f -THF1 GeneProduct :LOC_Os07g37250 Inositol phosphatase -OsAK GeneProduct :LOC_Os02g41590 Adenosine kinase -BADH2 GeneProduct :LOC_Os08g32870 SCENTED KERNEL 2 (fragrance) betaine-aldehyde dehydrogenase 2 -GPT1 GeneProduct :LOC_Os08g08840 -BEI GeneProduct :LOC_Os06g51084 expression diminished during grain filling at high temperatures -PHD zf GeneProduct :LOC_Os03g04980 -Male sterility protein GeneProduct :LOC_Os05g43040 -EF-1-g3 GeneProduct :LOC_Os06g37440 eEF-1B gamma 3 -LOC_Os08g04580 GeneProduct :LOC_Os08g04580 Thioredoxin -AOPBP-L GeneProduct :LOC_Os07g48570 -CRL1 GeneProduct :LOC_Os03g05510 -bZIP GeneProduct :LOC_Os11g06170 -CKX2/ Gn1a GeneProduct :LOC_Os01g10110 Cytokinin oxidase/dehydrogenase 2 -EIL1 GeneProduct :LOC_Os03g20780 -PHD Zn-finger GeneProduct :LOC_Os11g12650 -AHOX GeneProduct :LOC_Os10g39030 Associated with HOX family protein, expressed (UniProt Q8LN25)- Assigned as AHOX by Nemeth D and Hanumappa M (08/19/2010) -Smt1-1 GeneProduct :LOC_Os07g10600 Cycloartenol-C24-methyltransferase -SBEIIb GeneProduct :LOC_Os02g32660 expression diminished during grain filling at high temperatures -Acyl carrier GeneProduct :LOC_Os07g12150 -Fibrillin GeneProduct :LOC_Os09g04790 -OsLKR GeneProduct :LOC_Os02g54254 -NAC075 GeneProduct :LOC_Os01g09550 -VDAC5 GeneProduct :LOC_Os03g10510 -LTPL109 GeneProduct :LOC_Os07g37385 Extensin_2 -NAS1 GeneProduct :LOC_Os03g19427 NA synthase gene 1 -SCP40 GeneProduct :LOC_Os07g46350 Serine carboxypesidase -BTB-TAZ GeneProduct :LOC_Os01g66890 -HRGP GeneProduct :LOC_Os03g13560 Hydroxyproline-rich glycoprotein family protein-UniPret ID -YSL2 GeneProduct :LOC_Os02g43370 yellow stripe 1-like -RALF24 GeneProduct :LOC_Os11g26340 Rapid ALkalinization Factor -DUF584 GeneProduct :LOC_Os05g45450 -SuSy5 GeneProduct :LOC_Os02g58480 Sucrose synthase 5 -IDEF1 GeneProduct :LOC_Os08g01090 IDE-binding factor 2 -PSRR-L GeneProduct :LOC_Os07g25710 Phosphate starvation response regulator -FBL60 GeneProduct :LOC_Os12g33230 Leucine rich repeat -CYP450 GeneProduct :LOC_Os09g10340 -Integrase GeneProduct :LOC_Os11g11694 -MADS1 GeneProduct :LOC_Os03g11614 Also called LHS1 -Hydrolase GeneProduct :LOC_Os02g19650 Iron/ascorbate oxidoreductases -Phragmoplast kinase GeneProduct :LOC_Os04g28260 -WRKY 55 GeneProduct :LOC_Os03g20550 -Bam 2 GeneProduct :LOC_Os07g35940 -CycA1-1 GeneProduct :LOC_Os01g13260 -Retrotransposon GeneProduct :LOC_Os12g24050 Sulfotransferase -beta-fructofuranosidase GeneProduct :LOC_Os03g20020 Neutral/alkaline invertase 1 Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010) -FBK21 GeneProduct :LOC_Os10g21930 F-box domain and kelch repeat containing protein -MADS56 GeneProduct :LOC_Os10g39130 -HSP70 GeneProduct :LOC_Os12g14070 -PP2A2 GeneProduct :LOC_Os03g59060 -SUT3 GeneProduct :LOC_Os10g26470 -SSIVb GeneProduct :LOC_Os05g45720 -taxane 10-beta-hydroxylase GeneProduct :LOC_Os07g33480 Glutamate synthase cytochrome P450 domain containing protein -ENOD93-1 GeneProduct :LOC_Os06g05010 -EF-1-d1 GeneProduct :LOC_Os07g42300 EF-1B beta 1, EF-1-beta -DPE2 GeneProduct :LOC_Os07g46790 Also called ALK -ERG3 GeneProduct :LOC_Os04g44870 RPP16 -SIP2 GeneProduct :LOC_Os10g28350 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 1 Ethylene induced -Gal1 GeneProduct :LOC_Os10g35110 -SGT1 GeneProduct :LOC_Os01g43540 Responds to salicylic acid in chemically induced biotic response -Mald1-AP GeneProduct :LOC_Os01g56470 -GlyH GeneProduct :LOC_Os11g27400 Chitinase -VP1 GeneProduct :LOC_Os01g68370 Interaction with Wsi18 and Lea3 by orthology to H vulgare ABA-related Seed dormancy Interaction with Wsi18 and Lea3 by orthology to H vulgare -RCD1-L GeneProduct :LOC_Os04g52340 Also given LOC_Os07g37790 and LOC_Os03g57130 -IAA9 GeneProduct :LOC_Os02g56120 -vATP synthase C GeneProduct :LOC_Os05g51530 -GPT2-3 GeneProduct :LOC_Os07g33910 -OsPRP1 GeneProduct :LOC_Os10g05970 Proline rich protein -Amy2A GeneProduct :LOC_Os06g49970 ABA-repressible and GA-inducible -SNAC2 GeneProduct :LOC_Os01g66120 ABA-related -BT1-2 GeneProduct :LOC_Os02g10800 -Plasma membrane ATPase GeneProduct :LOC_Os04g56160 -IRO2 GeneProduct :LOC_Os01g72370 basic/helix-loop-helix 56 -ATP synthetase a GeneProduct :LOC_Os02g54624 -SPP2 GeneProduct :LOC_Os02g05030 sucrose-phosphatase 2 -MADS 8 GeneProduct :LOC_Os09g32948 Also called MADS 24 -SUS2 GeneProduct :LOC_Os06g09450 Sucrose synthase 2 -Ubi GeneProduct :LOC_Os09g31031 -MADS17 GeneProduct :LOC_Os04g49150 Also called NMADS3 and RMADS213 -C3H1 GeneProduct :LOC_Os01g07930 Zinc finger CCCH domain-containing protein Glutaredoxin-related -APL2 GeneProduct :LOC_Os01g44220 ADP-glucose Pyrophosphorylase large subunit 2, binding only happens with APS2b SSP genes examined was significantly suppressed in KD-RISBZ1/KD-RPBF expression diminished during grain filling at high temperatures -Mitrochondrial carrier GeneProduct :LOC_Os03g11510 -PGI-b GeneProduct :LOC_Os06g14510 -MADS 22 GeneProduct :LOC_Os02g52340 Also called RMD1 -GluC GeneProduct :LOC_Os02g15090 -ISA1 GeneProduct :LOC_Os08g40930 expression diminished during grain filling at high temperatures -E3-Ubi Ligase GeneProduct :LOC_Os05g47780 -DUF151 GeneProduct :LOC_Os01g50622 -PHOH GeneProduct :LOC_Os01g63270 Also called ALK -SUS3 GeneProduct :LOC_Os07g42490 Sucrose synthase 3 -Ring ZF GeneProduct :LOC_Os04g48050 -APS2a GeneProduct :LOC_Os08g25734 Also called AGPS2, ADP-glucose Pyrophosphorylase small subunit 2; SSP genes examined was significantly suppressed in KD-RISBZ1/KD-RPBF has two different transcripts= a:in leaf, b:in endosperm; binding with APL2 and Down regulation by RISBZ1 only happens with APS2b, binding with APL1 only happens with APS2a expression diminished during grain filling at high temperatures -Vin1 GeneProduct :LOC_Os04g45290 -CIN4 GeneProduct :LOC_Os01g73580 -RB GeneProduct :LOC_Os01g39580 seed coat color, endosperm color -NAC4 GeneProduct :LOC_Os01g60020 -MADS 15 GeneProduct :LOC_Os07g01820 Also called RAP1A -ISA3 GeneProduct :LOC_Os09g29404 -phosphomannomutase GeneProduct :LOC_Os06g28194 Soluble epoxide hydrolase -CIN7 GeneProduct :LOC_Os09g08072 -DAD1 GeneProduct :LOC_Os04g32550 Defender against cell death 1 -double-stranded beta-helix domain GeneProduct :LOC_Os11g06370 -MADS 16 GeneProduct :LOC_Os06g49840 -Bam 3 GeneProduct :LOC_Os07g35880 -IDI4 GeneProduct :LOC_Os09g28050 asparate aminotransferase -UGP2 GeneProduct :LOC_Os02g02560 -RPBF GeneProduct :LOC_Os02g15350 Functionaly redundant and compensatory expression between RISBZI and RPBF except for OsLKR/SDH double KD mutant (KD-RISBZ1/KD-RPBF) caused most expression change -SAL1 GeneProduct :LOC_Os06g43590 -Amy3D GeneProduct :LOC_Os08g36910 -PPR bZIP GeneProduct :LOC_Os05g40320 Symbol assigned by Nemeth D and Hanumappa M (08/19/2010) -TyrK GeneProduct :LOC_Os11g15340 SAM dependent carboxyl methyltransferase -LOC_Os06g14190 GeneProduct :LOC_Os06g14190 -AP-1gamma-1 GeneProduct :LOC_Os06g07090 -APS1 GeneProduct :LOC_Os09g12660 ADP-glucose Pyrophosphorylase small subunit 1  expression diminished during grain filling at high temperatures -GF14b GeneProduct :LOC_Os04g38870 -Amy1A GeneProduct :LOC_Os02g52710 -RACK1A GeneProduct :LOC_Os01g49290 Also called GPB-LR/ RWD -APT1 GeneProduct :LOC_Os12g39860 Adenine phosphoribosyltransferase 1 -Bam 1 GeneProduct :LOC_Os10g41550 -HOX6 GeneProduct :LOC_Os09g35910 Cooper et al. 2003 called this leucine zipper and misnamed HOX 22 as HOX 6 (22834) -TLR31 GeneProduct :LOC_Os02g53400 Translational repressor MPT5/PUF4 -PHOL GeneProduct :LOC_Os03g55090 -LOC_Os10g30450 GeneProduct :LOC_Os10g30450 Unknown-UniProt ID -APL3 GeneProduct :LOC_Os03g52460 -Sci2 GeneProduct :LOC_Os01g42860 -psbC GeneProduct :LOC_Os02g24632 -beta-1,3-Glucanase GeneProduct :LOC_Os03g25790 -Isocitrate lyase GeneProduct :LOC_Os07g34520 -MADS 57 GeneProduct :LOC_Os02g49840 -LOC_Os05g06330 GeneProduct :LOC_Os05g06330 -PUP2 GeneProduct :LOC_Os06g46740 -Oryzain gamma Protease GeneProduct :LOC_Os09g27030 -EF-1-g GeneProduct :LOC_Os02g12800 eEF-1G -RISBZ1 GeneProduct :LOC_Os07g08420 Functionaly redundant and compensatory expression between RISBZI and RPBF. Double Knock-Down mutant (KD-RISBZ1/KD-RPBF) caused most expression change in OsLKR/SDH -bip110 GeneProduct :LOC_Os06g08530 Putative ubiquitin-specific protease 23, BRI1-KD interacting protein 110 -SUT4 GeneProduct :LOC_Os02g58080 -Flavin containing monooxygenase 3-like GeneProduct :LOC_Os09g37620 Serine/threonine protein kinase -Ghd7 GeneProduct :LOC_Os07g15770 yield potential -Wsi18 GeneProduct :LOC_Os01g50910 Interaction with TRAB1 and VP1 by orthology to H vulgare ABA and GA induced water stress + cold stress member of the group 3 Lea family Wsi18 promoter is active in the whole grain -PGI-a GeneProduct :LOC_Os09g29070 -Wx1 GeneProduct :LOC_Os06g04200 30% less pre-mRNA in du1 mutant line Granule-bound starch synthase expression diminished during grain filling at high temperatures -GPT-A GeneProduct :LOC_Os05g07670 Assigned as GPT-A by Nemeth D and Hanumappa M (10/21/2010) -MADS 14 GeneProduct :LOC_Os03g54160 Also called AGL10, RAP1B -ABI5 GeneProduct :LOC_Os01g64000 -AOXDH GeneProduct :LOC_Os03g31550 -Serine protease GeneProduct :LOC_Os04g45910 Os04g0542900, -VP2-like GeneProduct :LOC_Os03g05750 -RAR1 GeneProduct :LOC_Os02g33180 -SUT1 GeneProduct :LOC_Os03g07480 -Flavin-containing monooxygenase GeneProduct :LOC_Os01g15540 -CSN5 GeneProduct :LOC_Os04g56070 -PROLM 24 GeneProduct :LOC_Os06g31070 16 kDa Prolamin -Importin alpha-1a GeneProduct :LOC_Os01g14950 NLS RECEPTOR -APRL3 GeneProduct :LOC_Os02g51850 Disulfide Isomerase -RAC GeneProduct :LOC_Os01g12900 -LOC_Os02g08530 GeneProduct :LOC_Os02g08530 Protein Kinase-UniProt ID -Anthranilate Phosphoribosyltransferase GeneProduct :LOC_Os03g03450 -Amy3B/Amy3C GeneProduct :LOC_Os09g28420 -DU1 GeneProduct :LOC_Os10g35550 dull endosperm-1 -Sci2 GeneProduct :LOC_Os01g42860 -Centromere protein GeneProduct :LOC_Os03g20580 -PIP5K GeneProduct :LOC_Os02g57660 Putative phosphatidylinositol-4-phosphate 5-kinase -REB GeneProduct :LOC_Os03g58250 Symbol assigned by Nemeth D and Hanumappa M (08/19/2010) -Lea3 GeneProduct :LOC_Os05g46480 Interaction with TRAB1 and VP1 by orthology to H vulgare ABA related -DPK4 GeneProduct :LOC_Os06g45300 Ser/thr/tyr kinase -LOC_Os10g40260 GeneProduct :LOC_Os10g40260 -Luc7-like 2 GeneProduct :LOC_Os03g62640 Sarcoplasmic reticulum -Jasmonate-induced protein GeneProduct :LOC_Os12g09700 Histone H3 (Lys9) methyltransferase -OsEM GeneProduct :LOC_Os05g28210 -SBEIIa GeneProduct :LOC_Os04g33460 expression diminished during grain filling at high temperatures -Ankyrin-like protein GeneProduct :LOC_Os09g17329 Iron transporter -Vin 2 GeneProduct :LOC_Os02g01590 -Bam 10 GeneProduct :LOC_Os03g22790 -ALDP GeneProduct :LOC_Os11g07020 Aldolase -GluA-1 GeneProduct :LOC_Os01g55690 -RCAA1 GeneProduct :LOC_Os11g47970 RuBisCO activase large isoform -PPDKB GeneProduct :LOC_Os05g33570 CPDK1, PPDKB -PSI-D GeneProduct :LOC_Os08g44680 -SSIVa GeneProduct :LOC_Os01g52250 Also called ALK -LOC_Os03g03860 GeneProduct :LOC_Os03g03860 Unknown-UniProt ID -PBZ1 GeneProduct :LOC_Os12g36880 -SSA2 GeneProduct :LOC_Os03g55730 10 kDa prolamin precursor - LOC_Os03g43910 GeneProduct :LOC_Os03g43910 -MADS5 GeneProduct :LOC_Os06g06750 -GLN1-1 GeneProduct :LOC_Os02g50240 Glutamine synthetase cytosolic isozyme 1-1, also called RGS28 and GS1;1 -MPK5 GeneProduct :LOC_Os03g17700 UniProt:MPK3, BIMK1, MAP3, MAPK2, MPK5 -HDS1 GeneProduct :LOC_Os02g39160 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 1 -SCR-like GeneProduct :LOC_Os02g45760 Scarecrow transcriptional regulator-like protein -CYP450 GeneProduct :LOC_Os10g08474 AP2 transcription factor -TRAB1 GeneProduct :LOC_Os08g36790 Interaction with Wsi18 and Lea3 by orthology to H vulgare bZIP transcription factor TRAB1, ABA RESPONSIVE ELEMENT 1=ABA1 -YSL15 GeneProduct :LOC_Os02g43410 YELLOW STRIPE LIKE 15 -ferroportin1 GeneProduct :LOC_Os06g36450 -LOC_Os03g55130 GeneProduct :LOC_Os03g55130 -Bam 9 GeneProduct :LOC_Os02g03690 -Photosystem I RC subunit GeneProduct :LOC_Os07g05480 -SSI GeneProduct :LOC_Os06g06560 -EXPB2 GeneProduct :LOC_Os10g40710 -Stress-related protein GeneProduct :LOC_Os07g47510 -Bam 8 GeneProduct :LOC_Os01g13550 -Phospholipase C GeneProduct :LOC_Os07g49330 -SUT5 GeneProduct :LOC_Os02g36700 -INV3 GeneProduct :LOC_Os02g32730 Neutral/alkaline invertase 3 Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010) -Delta-COP GeneProduct :LOC_Os01g61710 Delta coatamer -SSII-2 GeneProduct :LOC_Os02g51070 Also called ALK -Terpene cyclases GeneProduct :LOC_Os04g27190 -MCM2 GeneProduct :LOC_Os11g29380 -Rab21 GeneProduct :LOC_Os11g26790 ABA related water stress + cold stress -CML18 GeneProduct :LOC_Os05g13580 -GF14c GeneProduct :LOC_Os08g33370 -UGP1 GeneProduct :LOC_Os09g38030 -FDH GeneProduct :LOC_Os02g57040 Alcohol dehydrogenase class 3; Also called FALDH, GSH-FDH (Glutathione-dependent formaldehyde dehydrogenase) -LOC_Os05g50190 GeneProduct :LOC_Os05g50190 Protein Kinase-UniProt ID -LOC_Os04g41910 GeneProduct :LOC_Os04g41910 -RIR 1b GeneProduct :LOC_Os05g48260 -CPL1 GeneProduct :LOC_Os07g10690 Seed Shattering -FBO10 GeneProduct :LOC_Os11g34460 Adagio-like protein 3 Cytochrome P450 -OsCCP GeneProduct :LOC_Os12g08760 Assigned as OsCCP by Nemeth D and Hanumappa M (10/21/2010) carboxyvinyl-carboxyphosphonate phosphorylmutase -JA cmtr GeneProduct :LOC_Os06g22440 Putative S-adenosyl-L-methionine Subtilisin N-terminal Region -ISA2 GeneProduct :LOC_Os05g32710 -Bam 6 GeneProduct :LOC_Os09g39570 -PROLM28 GeneProduct :LOC_Os12g16890 Prolamin precursor, protein also called PPROL 17 -Pumilio GeneProduct :LOC_Os12g31000 Leucine rich repeat -IRT1 GeneProduct :LOC_Os03g46470 -Oligopeptide transporter 3 GeneProduct :LOC_Os03g54000 Isp4-like -MADS-box IL GeneProduct :LOC_Os02g54080 -ATP synthase GeneProduct :LOC_Os03g17070 -GluB-1A GeneProduct :LOC_Os02g15169 UniProt ID: P14323 -MLA10 GeneProduct :LOC_Os11g16470 Ankyrin repeat -RPK-TMK1 precursor GeneProduct :LOC_Os04g58910 receptor protein kinase TMK1 precursor -MADS 2 GeneProduct :LOC_Os01g66030 -LOC_Os12g37570 GeneProduct :LOC_Os12g37570 Protein Kinase-UniProt ID -DIP1 GeneProduct :LOC_Os05g34070 -EBP89 GeneProduct :LOC_Os03g08460 Also called EREBP1 -SUT2 GeneProduct :LOC_Os12g44380 -CycB1;1 GeneProduct :LOC_Os01g59120 Seed Shattering -SPP1 GeneProduct :LOC_Os01g27880 sucrose-phosphatase 1 -S-REP GeneProduct :LOC_Os04g47990 -bhlh113 GeneProduct :LOC_Os10g40740 basic/helix-loop-helix 113 -APL1 GeneProduct :LOC_Os05g50380 ADP-glucose Pyrophosphorylase large subunit 1 -CTR1-like GeneProduct :LOC_Os09g39320 Multitransmembrane protein -DREB1B GeneProduct :LOC_Os09g35010 -RUBQ1 GeneProduct :LOC_Os02g06640 Also called Polyubiquitin 6 Also given LOC_Os05g42424 which is not complete -NADPH G-3-P dh GeneProduct :LOC_Os08g34210 -Sdr4 GeneProduct :LOC_Os07g39700 -Ring Finger GeneProduct :LOC_Os01g01390 -SSIIc GeneProduct :LOC_Os10g30156 Also called ALK -LOC_Os04g57020 GeneProduct :LOC_Os04g57020 -PSII-OEP33 GeneProduct :LOC_Os01g31690 No symbol in gramene so OEP33 was assigned. 33kDa oxygen evolving protein of photosystem II -LOC_Os04g53350 GeneProduct :LOC_Os04g53350 Cooper 31122 ID -CRINKLY4 GeneProduct :LOC_Os08g28710 -RAG-1 GeneProduct :LOC_Os09g16260 RISBZ1 + RPBF activated the RAG-1 promoter greater than RPBF alone, though RISBZ1 did not independently affect promoter activity -CR4 GeneProduct :LOC_Os03g43670 homology with Crinkly4 -SSA1 GeneProduct :LOC_Os05g41970 26 kDa alpha globulin -TATC GeneProduct :LOC_Os01g31680 -DPE1 GeneProduct :LOC_Os07g43390 -LOC_Os02g53890 GeneProduct :LOC_Os02g53890 +Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI PubChem ChemSpider HMDB KEGG LipidMaps +HOX 22 GeneProduct :LOC_Os04g45810 "In Cooper et al. 2003 protein sequence provided matches HOX 22, however it was named HOX6 (AF145730)" +Dynamin GeneProduct :LOC_Os06g13820 "" +IAA amidohydrolase GeneProduct :LOC_Os03g62060 "" +HSP40 GeneProduct :LOC_Os03g44620 "" +bHLH60 GeneProduct :LOC_Os08g04390 "Helix-loop-helix TF " +MADS 18 GeneProduct :LOC_Os07g41370 "Also called MADS 28" +PPDKB GeneProduct :LOC_Os05g33570 "Involved in grain filling" +2-d-3-D phosphooctonate aldolase GeneProduct :LOC_Os12g10784 "" +GB2 GeneProduct :LOC_Os03g57960 "Globulin 2" +BTB/POZ GeneProduct :LOC_Os10g29390 "2-keto-3-deoxy-6-phosphogluconate aldolase" +LOC_Os06g39906 GeneProduct :LOC_Os06g39906 "" +NB-ARC domain protein GeneProduct :LOC_Os11g34880 "Jacalin" +ZF-like GeneProduct :LOC_Os01g40990 "" +grpA3 GeneProduct :LOC_Os05g02780 "" +EXPB4 GeneProduct :LOC_Os10g40730 "Beta-expansin-4" +Bam 4 GeneProduct :LOC_Os07g47120 "" +Pyrrolidone-Carboxylpeptidase GeneProduct :LOC_Os03g25270 "" +SPS-O spp GeneProduct :LOC_Os08g20660 "sucrose-phosphate synthase-Oncidium spp= named after table III on Yamakawa et al. (2007) " +IAA4 GeneProduct :LOC_Os01g18360 "" +Cyp2 GeneProduct :LOC_Os02g02890 "" +Bam 7 GeneProduct :LOC_Os03g04770 "" +Thioredoxin-like GeneProduct :LOC_Os04g57310 "thiol-disulphide oxidoreductase DCC" +Shaggy kinase GeneProduct :LOC_Os10g37740 "" +Pto kinase Interactor 1 GeneProduct :LOC_Os05g04520 "" +LOC_Os09g38090 GeneProduct :LOC_Os09g38090 "" +PCNA GeneProduct :LOC_Os02g56130 "Proliferating cell nuclear antigen expressed strongly in the shoot apical meristem" +GDSL-like Lipase GeneProduct :LOC_Os10g05088 "SGNH_plant_lipase" +PP2A-3 GeneProduct :LOC_Os02g12580 "" +TRNA endonuclease GeneProduct :LOC_Os11g38930 "catalytic C-terminal domain containing protein" +SSIVb GeneProduct :LOC_Os05g45720 "Also called ALK" +UDP-glucosyl transferase GeneProduct :LOC_Os04g12960 "" +WRKY 51 GeneProduct :LOC_Os04g21950 "ABA-inducible & GA-repressible WRKY 51 by itself also represses activation of Amy2A by GAMYB" +RSR1 GeneProduct :LOC_Os01g40280 "" +RAD6 GeneProduct :LOC_Os03g57790 "transcripts of both OsRad6 and OsSgt1 were found to be strongly expressed in the proliferating tissues such SAM" +HAD-like GeneProduct :LOC_Os03g16670 "" +Myosin like GeneProduct :LOC_Os05g02820 "" +SAM cmtr GeneProduct :LOC_Os02g06770 "" +Kinesin GeneProduct :LOC_Os03g43100 "" +SSIIIb GeneProduct :LOC_Os04g53310 "Also called ALK" + EF-1-d2 GeneProduct :LOC_Os03g29260 "Elongation factor 1 beta 2" +Keto acyl CoA thiolase GeneProduct :LOC_Os02g57260 "" +OsFBX237 GeneProduct :LOC_Os07g35050 "Cdc2-related protein kinase" +ZIP-1a GeneProduct :LOC_Os12g13170 "" +eif(iso)4g GeneProduct :LOC_Os04g42140 "" +Fructose-6-phosphate 1-phosphotransferase GeneProduct :LOC_Os08g25720 "" +GluA-3 GeneProduct :LOC_Os03g31360 "" +RAV1-like GeneProduct :LOC_Os01g49830 "" +LEA 14-A GeneProduct :LOC_Os05g50710 "" +GABA permease GeneProduct :LOC_Os01g71720 "Amino acid/polyamine transporter " +OsIAA13 GeneProduct :LOC_Os03g53150 "" +OSE2 GeneProduct :LOC_Os01g64730 "bZIP transcription factor domain containing protein" +MAPK2 GeneProduct :LOC_Os02g05480 "UniProt:MAPK2, BIMK1, MAP3, MAPK5, MPK3, MSRMK2" +IDI2 GeneProduct :LOC_Os11g11050 "Initiation factor 2 subunit family protein" +AP37 GeneProduct :LOC_Os01g58420 "" +SNAC1 GeneProduct :LOC_Os03g60080 "" +IDS1/ MT4A GeneProduct :LOC_Os12g38270 "" +GBSSII GeneProduct :LOC_Os07g22930 "Also called ALK" +Ser/thr PK GeneProduct :LOC_Os06g04880 "" +LOC_Os03g50390 GeneProduct :LOC_Os03g50390 "Protein Kinase-UniProt ID" +PRP1 GeneProduct :LOC_Os05g13940 "" +INV2 GeneProduct :LOC_Os01g22900 "Neutral/alkaline invertase 2 Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010)" +Phosphoglucomutase GeneProduct :LOC_Os05g48200 "" + EPSPS1 GeneProduct :LOC_Os06g04280 "5-Enolpyruvylshikimate-3-phosphate synthase 1" +APL4/ AGPL4 GeneProduct :LOC_Os07g13980 "" +CycD2-2 GeneProduct :LOC_Os07g42860 "" +Amy3A GeneProduct :LOC_Os09g28400 "" +TPR-PK GeneProduct :LOC_Os03g61010 "Putative protein kinase " +SPS-Zm GeneProduct :LOC_Os06g42824 "sucrose-phosphate synthase-Zea mays= named after table III on Yamakawa et al. (2007) " +FERTILLIN GeneProduct :LOC_Os06g01650 "" +Disease resistance-like GeneProduct :LOC_Os12g40490 "LIM domain-containing protein, putative, expressed" +bip129 GeneProduct :LOC_Os08g40790 "" +KOB1 GeneProduct :LOC_Os02g57240 "Probable voltage-gated potassium channel subunit beta" +GP-alpha-1 GeneProduct :LOC_Os05g26890 "G-alpha protein also called GPA1/D1/GA1" +DAHPS1 GeneProduct :LOC_Os03g27230 "3-deoxy-D-arabino heptulosonate-7-phosphate synthase 1 " +NAAT1 GeneProduct :LOC_Os02g20360 "nicotianamine aminotransferase " +NAC5 GeneProduct :LOC_Os11g08210 "ABA related" +SSIIIa/ Flo5 GeneProduct :LOC_Os08g09230 "expression diminished during grain filling at high temperatures " +Amy4A GeneProduct :LOC_Os01g51754 "" +NAC2 GeneProduct :LOC_Os02g57650 "" +U2 snRNP GeneProduct :LOC_Os11g41820 "" +SPS-So GeneProduct :LOC_Os06g43630 "sucrose-phosphate synthase-Saccharum officinarum= named after table III on Yamakawa et al. (2007) " +Pr1b GeneProduct :LOC_Os01g28450 "" +GluA-2 GeneProduct :LOC_Os10g26060 "" +MTN GeneProduct :LOC_Os06g02220 "Methylthioadenosine/S-adenosyl homocysteine nucleosidase" +RPS20 GeneProduct :LOC_Os06g04290 "P35686 " +Phosphotyrosine GeneProduct :LOC_Os08g44320 "" +Ser/thr PK GeneProduct :LOC_Os02g43290 "" +ZOS1-15 GeneProduct :LOC_Os01g62190 "Salt-stress ABA related" +MADS7/45 GeneProduct :LOC_Os08g41950 "also called MADS 45, AGL6, M79" +ARD2 GeneProduct :LOC_Os03g06620 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 2; Also called IDI1 and SIP2A" +GAMYB GeneProduct :LOC_Os01g59660 "regulates GA induction of Amy2A" +ALDH7 GeneProduct :LOC_Os09g26880 "Needed for seed maturation and viability. Expression Patterns during Seed Development Correspond with Pigment Accumulation Patterns in Seeds Plays a role in the removal of MDA that forms during seed desiccation" +DOF ZF GeneProduct :LOC_Os02g49440 "" +WRKY 71 GeneProduct :LOC_Os02g08440 "ABA-inducible & GA-repressible Interaction between WRKY 51 and 71 enhances the binding affinity of WRKY71 to the Amy32b promoter WRKY 71 by itself also represses activation of Amy2A by GAMYB" +Complex 1L GeneProduct :LOC_Os06g50000 "Assigned as Complex 1L by Nemeth D and Hanumappa M (10/21/2010) complex 1 family protein-like (LYR family)" +PP2A-B GeneProduct :LOC_Os05g40350 "" +GF14A GeneProduct :LOC_Os08g37490 "WIN2, WIP2" +PROLM26 GeneProduct :LOC_Os07g10580 "Prolamin precursor, also called RP5" +MT2b GeneProduct :LOC_Os05g02070 "" +IAA1 GeneProduct :LOC_Os01g08320 "" +LOC_Os01g14110 GeneProduct :LOC_Os01g14110 "Assigned as bHLH-tf by Nemeth D and Hanumappa M (10/21/2010)" +TAP46 GeneProduct :LOC_Os12g04290 "" +PIT GeneProduct :LOC_Os01g05620 "" +Permease GeneProduct :LOC_Os07g04180 "" +SSII-3 GeneProduct :LOC_Os06g12450 "expression diminished during grain filling at high temperatures " +SuSy6 GeneProduct :LOC_Os04g24430 "Sucrose synthase 6 " +NAC 10 GeneProduct :LOC_Os11g03300 "" +Myosin like GeneProduct :LOC_Os03g16120 "" +Sub9 GeneProduct :LOC_Os01g58290 "Amino acid transporters" +DUF630 GeneProduct :LOC_Os10g41310 "Symbol assigned by Nemeth D and Hanumappa M (08/19/2010)" +CACTA, En/Spm GeneProduct :LOC_Os01g09220 "" +CDKA-2 GeneProduct :LOC_Os02g03060 "" +PHT4;3 GeneProduct :LOC_Os01g63290 "Na+ dep inorg phosphate cotransporter " +Oryzain alpha Protease GeneProduct :LOC_Os04g55650 "" +msrB-1 GeneProduct :LOC_Os03g24600 "2 more IDs found on Gramene. Hence called 1, 2 and 3 to differentiate. LOC_Os06g27760=msrB-2, LOC_Os05g33510=msrB-3 (D Nemeth and M Hanumappa 08/17/2010)." +GTP cyclohydrolase GeneProduct :LOC_Os05g38570 "GTP cyclohydrolase II/3,4-dihydroxy-2-butanone-4-phosphate synthase" +Ubiquitin proteinase GeneProduct :LOC_Os02g43760 "ubiquitin carboxyl-terminal hydrolase, family 1, putative, expressed" +PP2A1 GeneProduct :LOC_Os06g37660 "" +LOC_Os01g62740 GeneProduct :LOC_Os01g62740 "" +Bam 5 GeneProduct :LOC_Os10g32810 "" +AP2 domain GeneProduct :LOC_Os03g64260 "" +SET domain protein GeneProduct :LOC_Os02g40770 "histone-lysine N-methyltransferase" +UOS1 GeneProduct :LOC_Os06g49120 "NAD(P)-binding/Rossman fold" +SPK GeneProduct :LOC_Os10g39420 "required for storage product accumulation during seed development seed-specific protein kinase" +MADS 3 GeneProduct :LOC_Os01g10504 "Also called RAG" +USP1 GeneProduct :LOC_Os07g47620 "ETFP adenine nucleotide" +LOC_Os03g56940 GeneProduct :LOC_Os03g56940 "" +GPT2-B GeneProduct :LOC_Os01g07310 "Assigned as GPT-B by Nemeth D and Hanumappa M (10/21/2010)" +BT1-1 GeneProduct :LOC_Os05g07900 "" +SPS-Hv GeneProduct :LOC_Os02g09170 "sucrose-phosphate synthase-Hordeum vulgare= named after table III on Yamakawa et al. (2007) " +LPLA GeneProduct :LOC_Os08g33810 "" +NAS2 GeneProduct :LOC_Os03g19420 "NA synthase gene 2 " +GW2 GeneProduct :LOC_Os02g14720 "encodes a RING protein with E3 ubiquitin ligase activity" +GDSL-like Lipase GeneProduct :LOC_Os01g11650 "" +ARF1 GeneProduct :LOC_Os11g32110 "" +UGP GeneProduct :LOC_Os02g02550 "" +DEP GeneProduct :LOC_Os11g29370 "Haloacid dehalogenase-like hydrolase family protein" +flavanone 3-hydroxylase GeneProduct :LOC_Os08g37456 "2-oxoglutarate (2OG) - Fe(II) oxygenase " +BBTI4 GeneProduct :LOC_Os01g03340 "Bowman-Birk type bran trypsin inhibitor " +HMG1 GeneProduct :LOC_Os06g51220 "" +PPROL 14 E GeneProduct :LOC_Os05g26377 "13 kDa Prolamin, also called PPROL 14, PPROL 4A, PPROL 7, PG5a, PROLM 8, PROLM 9, UniProt ID: Q95737" +CIN1 GeneProduct :LOC_Os02g33110 "" +ADP ribosylation GTPase GeneProduct :LOC_Os03g17020 "" +MADS 6 GeneProduct :LOC_Os02g45770 "Also called MFO1" +GLUB4 GeneProduct :LOC_Os02g16830 "" +SuSy4 GeneProduct :LOC_Os03g22120 "Sucrose synthase 4 " +GF14-e GeneProduct :LOC_Os02g36974 "" +CDKA-1 GeneProduct :LOC_Os03g02680 "" +IDEF2 GeneProduct :LOC_Os05g35170 "IDE-binding factor 2 " +SUS1 GeneProduct :LOC_Os03g28330 "Sucrose synthase 1 " +LOC_Os01g12080 GeneProduct :LOC_Os01g12080 "" +Amy3E GeneProduct :LOC_Os08g36900 "" +prx61 GeneProduct :LOC_Os04g59190 "Class III peroxidase 61" +MADS13 GeneProduct :LOC_Os12g10540 "Also called MAF1" +SWEET3a GeneProduct :LOC_Os05g12320 "" +BEIII GeneProduct :LOC_Os06g26234 "" +Pectinesterase GeneProduct :LOC_Os07g02810 "" +VIP1-like GeneProduct :LOC_Os06g02240 "" +AREB GeneProduct :LOC_Os05g41070 "" +PPDKA GeneProduct :LOC_Os03g31750 "Assigned as GPT-B by Nemeth D and Hanumappa M (10/21/2010)" +PUL GeneProduct :LOC_Os04g08270 "expression diminished during grain filling at high temperatures" +CCT/B-box zinc finger GeneProduct :LOC_Os02g49230 "" +CIN3 GeneProduct :LOC_Os04g33720 "" +TUBB3 GeneProduct :LOC_Os06g46000 "Tubulin beta-3 chain" +ACO1 GeneProduct :LOC_Os09g27750 "" +SAP11 GeneProduct :LOC_Os08g39450 "Also called ZFP60" +MADS47 GeneProduct :LOC_Os03g08754 "Also called MDP" +KRP3 GeneProduct :LOC_Os11g40030 "" +DMAS1 GeneProduct :LOC_Os03g13390 "Deoxymugineic acid synthase1 " +CIN5 GeneProduct :LOC_Os04g56930 "" +LOC_Os03g07360 GeneProduct :LOC_Os03g07360 "" +RIC1 GeneProduct :LOC_Os01g37800 "" +RBCL GeneProduct :LOC_Os10g21268 "" +CIN2 GeneProduct :LOC_Os04g33740 "" +DEK1 GeneProduct :LOC_Os02g48000 "" +RA GeneProduct :LOC_Os04g47080 "seed coat color, endosperm color" +HSP90 GeneProduct :LOC_Os09g30418 "Also called HSP81-2" +GF14F GeneProduct :LOC_Os03g50290 "G-box factor 14-3-3 f" +THF1 GeneProduct :LOC_Os07g37250 "Inositol phosphatase" +OsAK GeneProduct :LOC_Os02g41590 "Adenosine kinase " +BADH2 GeneProduct :LOC_Os08g32870 "SCENTED KERNEL 2 (fragrance) betaine-aldehyde dehydrogenase 2" +GPT1 GeneProduct :LOC_Os08g08840 "" +BEI GeneProduct :LOC_Os06g51084 "expression diminished during grain filling at high temperatures" +PHD zf GeneProduct :LOC_Os03g04980 "" +Male sterility protein GeneProduct :LOC_Os05g43040 "" +EF-1-g3 GeneProduct :LOC_Os06g37440 "eEF-1B gamma 3" +LOC_Os08g04580 GeneProduct :LOC_Os08g04580 "Thioredoxin" +AOPBP-L GeneProduct :LOC_Os07g48570 "" +CRL1 GeneProduct :LOC_Os03g05510 "" +bZIP GeneProduct :LOC_Os11g06170 "" +CKX2/ Gn1a GeneProduct :LOC_Os01g10110 "Cytokinin oxidase/dehydrogenase 2 " +EIL1 GeneProduct :LOC_Os03g20780 "" +PHD Zn-finger GeneProduct :LOC_Os11g12650 "" +AHOX GeneProduct :LOC_Os10g39030 "Associated with HOX family protein, expressed (UniProt Q8LN25)- Assigned as AHOX by Nemeth D and Hanumappa M (08/19/2010)" +Smt1-1 GeneProduct :LOC_Os07g10600 "Cycloartenol-C24-methyltransferase" +SBEIIb GeneProduct :LOC_Os02g32660 "expression diminished during grain filling at high temperatures" +Acyl carrier GeneProduct :LOC_Os07g12150 "" +Fibrillin GeneProduct :LOC_Os09g04790 "" +OsLKR GeneProduct :LOC_Os02g54254 "" +NAC075 GeneProduct :LOC_Os01g09550 "" +VDAC5 GeneProduct :LOC_Os03g10510 "" +LTPL109 GeneProduct :LOC_Os07g37385 "Extensin_2 " +NAS1 GeneProduct :LOC_Os03g19427 "NA synthase gene 1 " +SCP40 GeneProduct :LOC_Os07g46350 "Serine carboxypesidase" +BTB-TAZ GeneProduct :LOC_Os01g66890 "" +HRGP GeneProduct :LOC_Os03g13560 "Hydroxyproline-rich glycoprotein family protein-UniPret ID" +YSL2 GeneProduct :LOC_Os02g43370 "yellow stripe 1-like " +RALF24 GeneProduct :LOC_Os11g26340 "Rapid ALkalinization Factor" +DUF584 GeneProduct :LOC_Os05g45450 "" +SuSy5 GeneProduct :LOC_Os02g58480 "Sucrose synthase 5 " +IDEF1 GeneProduct :LOC_Os08g01090 "IDE-binding factor 2" +PSRR-L GeneProduct :LOC_Os07g25710 "Phosphate starvation response regulator " +FBL60 GeneProduct :LOC_Os12g33230 "Leucine rich repeat " +CYP450 GeneProduct :LOC_Os09g10340 "" +Integrase GeneProduct :LOC_Os11g11694 "" +MADS1 GeneProduct :LOC_Os03g11614 "Also called LHS1" +Hydrolase GeneProduct :LOC_Os02g19650 "Iron/ascorbate oxidoreductases" +Phragmoplast kinase GeneProduct :LOC_Os04g28260 "" +WRKY 55 GeneProduct :LOC_Os03g20550 "" +Bam 2 GeneProduct :LOC_Os07g35940 "" +CycA1-1 GeneProduct :LOC_Os01g13260 "" +Retrotransposon GeneProduct :LOC_Os12g24050 "Sulfotransferase" +beta-fructofuranosidase GeneProduct :LOC_Os03g20020 "Neutral/alkaline invertase 1 Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010)" +FBK21 GeneProduct :LOC_Os10g21930 "F-box domain and kelch repeat containing protein" +MADS56 GeneProduct :LOC_Os10g39130 "" +HSP70 GeneProduct :LOC_Os12g14070 "" +PP2A2 GeneProduct :LOC_Os03g59060 "" +SUT3 GeneProduct :LOC_Os10g26470 "" +SSIVb GeneProduct :LOC_Os05g45720 "" +taxane 10-beta-hydroxylase GeneProduct :LOC_Os07g33480 "Glutamate synthase cytochrome P450 domain containing protein" +ENOD93-1 GeneProduct :LOC_Os06g05010 "" +EF-1-d1 GeneProduct :LOC_Os07g42300 "EF-1B beta 1, EF-1-beta" +DPE2 GeneProduct :LOC_Os07g46790 "Also called ALK" +ERG3 GeneProduct :LOC_Os04g44870 "RPP16" +SIP2 GeneProduct :LOC_Os10g28350 "1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 1 Ethylene induced" +Gal1 GeneProduct :LOC_Os10g35110 "" +SGT1 GeneProduct :LOC_Os01g43540 "Responds to salicylic acid in chemically induced biotic response" +Mald1-AP GeneProduct :LOC_Os01g56470 "" +GlyH GeneProduct :LOC_Os11g27400 "Chitinase" +VP1 GeneProduct :LOC_Os01g68370 "Interaction with Wsi18 and Lea3 by orthology to H vulgare ABA-related Seed dormancy Interaction with Wsi18 and Lea3 by orthology to H vulgare" +RCD1-L GeneProduct :LOC_Os04g52340 "Also given LOC_Os07g37790 and LOC_Os03g57130" +IAA9 GeneProduct :LOC_Os02g56120 "" +vATP synthase C GeneProduct :LOC_Os05g51530 "" +GPT2-3 GeneProduct :LOC_Os07g33910 "" +OsPRP1 GeneProduct :LOC_Os10g05970 "Proline rich protein" +Amy2A GeneProduct :LOC_Os06g49970 "ABA-repressible and GA-inducible" +SNAC2 GeneProduct :LOC_Os01g66120 "ABA-related" +BT1-2 GeneProduct :LOC_Os02g10800 "" +Plasma membrane ATPase GeneProduct :LOC_Os04g56160 "" +IRO2 GeneProduct :LOC_Os01g72370 "basic/helix-loop-helix 56 " +ATP synthetase a GeneProduct :LOC_Os02g54624 "" +SPP2 GeneProduct :LOC_Os02g05030 "sucrose-phosphatase 2 " +MADS 8 GeneProduct :LOC_Os09g32948 "Also called MADS 24" +SUS2 GeneProduct :LOC_Os06g09450 "Sucrose synthase 2 " +Ubi GeneProduct :LOC_Os09g31031 "" +MADS17 GeneProduct :LOC_Os04g49150 "Also called NMADS3 and RMADS213" +C3H1 GeneProduct :LOC_Os01g07930 "Zinc finger CCCH domain-containing protein Glutaredoxin-related " +APL2 GeneProduct :LOC_Os01g44220 "ADP-glucose Pyrophosphorylase large subunit 2, binding only happens with APS2b SSP genes examined was significantly suppressed in KD-RISBZ1/KD-RPBF expression diminished during grain filling at high temperatures" +Mitrochondrial carrier GeneProduct :LOC_Os03g11510 "" +PGI-b GeneProduct :LOC_Os06g14510 "" +MADS 22 GeneProduct :LOC_Os02g52340 "Also called RMD1" +GluC GeneProduct :LOC_Os02g15090 "" +ISA1 GeneProduct :LOC_Os08g40930 "expression diminished during grain filling at high temperatures " +E3-Ubi Ligase GeneProduct :LOC_Os05g47780 "" +DUF151 GeneProduct :LOC_Os01g50622 "" +PHOH GeneProduct :LOC_Os01g63270 "Also called ALK" +SUS3 GeneProduct :LOC_Os07g42490 "Sucrose synthase 3 " +Ring ZF GeneProduct :LOC_Os04g48050 "" +APS2a GeneProduct :LOC_Os08g25734 "Also called AGPS2, ADP-glucose Pyrophosphorylase small subunit 2; SSP genes examined was significantly suppressed in KD-RISBZ1/KD-RPBF has two different transcripts= a:in leaf, b:in endosperm; binding with APL2 and Down regulation by RISBZ1 only happens with APS2b, binding with APL1 only happens with APS2a expression diminished during grain filling at high temperatures" +Vin1 GeneProduct :LOC_Os04g45290 "" +CIN4 GeneProduct :LOC_Os01g73580 "" +RB GeneProduct :LOC_Os01g39580 "seed coat color, endosperm color" +NAC4 GeneProduct :LOC_Os01g60020 "" +MADS 15 GeneProduct :LOC_Os07g01820 "Also called RAP1A" +ISA3 GeneProduct :LOC_Os09g29404 "" +phosphomannomutase GeneProduct :LOC_Os06g28194 "Soluble epoxide hydrolase" +CIN7 GeneProduct :LOC_Os09g08072 "" +DAD1 GeneProduct :LOC_Os04g32550 "Defender against cell death 1" +double-stranded beta-helix domain GeneProduct :LOC_Os11g06370 "" +MADS 16 GeneProduct :LOC_Os06g49840 "" +Bam 3 GeneProduct :LOC_Os07g35880 "" +IDI4 GeneProduct :LOC_Os09g28050 "asparate aminotransferase" +UGP2 GeneProduct :LOC_Os02g02560 "" +RPBF GeneProduct :LOC_Os02g15350 "Functionaly redundant and compensatory expression between RISBZI and RPBF except for OsLKR/SDH double KD mutant (KD-RISBZ1/KD-RPBF) caused most expression change" +SAL1 GeneProduct :LOC_Os06g43590 "" +Amy3D GeneProduct :LOC_Os08g36910 "" +PPR bZIP GeneProduct :LOC_Os05g40320 "Symbol assigned by Nemeth D and Hanumappa M (08/19/2010)" +TyrK GeneProduct :LOC_Os11g15340 "SAM dependent carboxyl methyltransferase" +LOC_Os06g14190 GeneProduct :LOC_Os06g14190 "" +AP-1gamma-1 GeneProduct :LOC_Os06g07090 "" +APS1 GeneProduct :LOC_Os09g12660 "ADP-glucose Pyrophosphorylase small subunit 1  expression diminished during grain filling at high temperatures" +GF14b GeneProduct :LOC_Os04g38870 "" +Amy1A GeneProduct :LOC_Os02g52710 "" +RACK1A GeneProduct :LOC_Os01g49290 "Also called GPB-LR/ RWD" +APT1 GeneProduct :LOC_Os12g39860 "Adenine phosphoribosyltransferase 1" +Bam 1 GeneProduct :LOC_Os10g41550 "" +HOX6 GeneProduct :LOC_Os09g35910 "Cooper et al. 2003 called this leucine zipper and misnamed HOX 22 as HOX 6 (22834)" +TLR31 GeneProduct :LOC_Os02g53400 "Translational repressor MPT5/PUF4" +PHOL GeneProduct :LOC_Os03g55090 "" +LOC_Os10g30450 GeneProduct :LOC_Os10g30450 "Unknown-UniProt ID" +APL3 GeneProduct :LOC_Os03g52460 "" +Sci2 GeneProduct :LOC_Os01g42860 "" +psbC GeneProduct :LOC_Os02g24632 "" +beta-1,3-Glucanase GeneProduct :LOC_Os03g25790 "" +Isocitrate lyase GeneProduct :LOC_Os07g34520 "" +MADS 57 GeneProduct :LOC_Os02g49840 "" +LOC_Os05g06330 GeneProduct :LOC_Os05g06330 "" +PUP2 GeneProduct :LOC_Os06g46740 "" +Oryzain gamma Protease GeneProduct :LOC_Os09g27030 "" +EF-1-g GeneProduct :LOC_Os02g12800 "eEF-1G" +RISBZ1 GeneProduct :LOC_Os07g08420 "Functionaly redundant and compensatory expression between RISBZI and RPBF. Double Knock-Down mutant (KD-RISBZ1/KD-RPBF) caused most expression change in OsLKR/SDH" +bip110 GeneProduct :LOC_Os06g08530 "Putative ubiquitin-specific protease 23, BRI1-KD interacting protein 110" +SUT4 GeneProduct :LOC_Os02g58080 "" +Flavin containing monooxygenase 3-like GeneProduct :LOC_Os09g37620 "Serine/threonine protein kinase" +Ghd7 GeneProduct :LOC_Os07g15770 "yield potential" +Wsi18 GeneProduct :LOC_Os01g50910 "Interaction with TRAB1 and VP1 by orthology to H vulgare ABA and GA induced water stress + cold stress member of the group 3 Lea family Wsi18 promoter is active in the whole grain" +PGI-a GeneProduct :LOC_Os09g29070 "" +Wx1 GeneProduct :LOC_Os06g04200 "30% less pre-mRNA in du1 mutant line Granule-bound starch synthase expression diminished during grain filling at high temperatures" +GPT-A GeneProduct :LOC_Os05g07670 "Assigned as GPT-A by Nemeth D and Hanumappa M (10/21/2010)" +MADS 14 GeneProduct :LOC_Os03g54160 "Also called AGL10, RAP1B" +ABI5 GeneProduct :LOC_Os01g64000 "" +AOXDH GeneProduct :LOC_Os03g31550 "" +Serine protease GeneProduct :LOC_Os04g45910 "Os04g0542900, " +VP2-like GeneProduct :LOC_Os03g05750 "" +RAR1 GeneProduct :LOC_Os02g33180 "" +SUT1 GeneProduct :LOC_Os03g07480 "" +Flavin-containing monooxygenase GeneProduct :LOC_Os01g15540 "" +CSN5 GeneProduct :LOC_Os04g56070 "" +PROLM 24 GeneProduct :LOC_Os06g31070 "16 kDa Prolamin" +Importin alpha-1a GeneProduct :LOC_Os01g14950 "NLS RECEPTOR " +APRL3 GeneProduct :LOC_Os02g51850 "Disulfide Isomerase " +RAC GeneProduct :LOC_Os01g12900 "" +LOC_Os02g08530 GeneProduct :LOC_Os02g08530 "Protein Kinase-UniProt ID" +Anthranilate Phosphoribosyltransferase GeneProduct :LOC_Os03g03450 "" +Amy3B/Amy3C GeneProduct :LOC_Os09g28420 "" +DU1 GeneProduct :LOC_Os10g35550 "dull endosperm-1" +Centromere protein GeneProduct :LOC_Os03g20580 "" +PIP5K GeneProduct :LOC_Os02g57660 "Putative phosphatidylinositol-4-phosphate 5-kinase" +REB GeneProduct :LOC_Os03g58250 "Symbol assigned by Nemeth D and Hanumappa M (08/19/2010)" +Lea3 GeneProduct :LOC_Os05g46480 "Interaction with TRAB1 and VP1 by orthology to H vulgare ABA related" +DPK4 GeneProduct :LOC_Os06g45300 "Ser/thr/tyr kinase " +LOC_Os10g40260 GeneProduct :LOC_Os10g40260 "" +Luc7-like 2 GeneProduct :LOC_Os03g62640 "Sarcoplasmic reticulum " +Jasmonate-induced protein GeneProduct :LOC_Os12g09700 "Histone H3 (Lys9) methyltransferase" +OsEM GeneProduct :LOC_Os05g28210 "" +SBEIIa GeneProduct :LOC_Os04g33460 "expression diminished during grain filling at high temperatures" +Ankyrin-like protein GeneProduct :LOC_Os09g17329 "Iron transporter" +Vin 2 GeneProduct :LOC_Os02g01590 "" +Bam 10 GeneProduct :LOC_Os03g22790 "" +ALDP GeneProduct :LOC_Os11g07020 "Aldolase " +GluA-1 GeneProduct :LOC_Os01g55690 "" +RCAA1 GeneProduct :LOC_Os11g47970 "RuBisCO activase large isoform" +PPDKB GeneProduct :LOC_Os05g33570 "CPDK1, PPDKB" +PSI-D GeneProduct :LOC_Os08g44680 "" +SSIVa GeneProduct :LOC_Os01g52250 "Also called ALK" +LOC_Os03g03860 GeneProduct :LOC_Os03g03860 "Unknown-UniProt ID" +PBZ1 GeneProduct :LOC_Os12g36880 "" +SSA2 GeneProduct :LOC_Os03g55730 "10 kDa prolamin precursor" + LOC_Os03g43910 GeneProduct :LOC_Os03g43910 "" +MADS5 GeneProduct :LOC_Os06g06750 "" +GLN1-1 GeneProduct :LOC_Os02g50240 "Glutamine synthetase cytosolic isozyme 1-1, also called RGS28 and GS1;1" +MPK5 GeneProduct :LOC_Os03g17700 "UniProt:MPK3, BIMK1, MAP3, MAPK2, MPK5" +HDS1 GeneProduct :LOC_Os02g39160 "4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 1" +SCR-like GeneProduct :LOC_Os02g45760 "Scarecrow transcriptional regulator-like protein" +CYP450 GeneProduct :LOC_Os10g08474 "AP2 transcription factor" +TRAB1 GeneProduct :LOC_Os08g36790 "Interaction with Wsi18 and Lea3 by orthology to H vulgare bZIP transcription factor TRAB1, ABA RESPONSIVE ELEMENT 1=ABA1" +YSL15 GeneProduct :LOC_Os02g43410 "YELLOW STRIPE LIKE 15" +ferroportin1 GeneProduct :LOC_Os06g36450 "" +LOC_Os03g55130 GeneProduct :LOC_Os03g55130 "" +Bam 9 GeneProduct :LOC_Os02g03690 "" +Photosystem I RC subunit GeneProduct :LOC_Os07g05480 "" +SSI GeneProduct :LOC_Os06g06560 "" +EXPB2 GeneProduct :LOC_Os10g40710 "" +Stress-related protein GeneProduct :LOC_Os07g47510 "" +Bam 8 GeneProduct :LOC_Os01g13550 "" +Phospholipase C GeneProduct :LOC_Os07g49330 "" +SUT5 GeneProduct :LOC_Os02g36700 "" +INV3 GeneProduct :LOC_Os02g32730 "Neutral/alkaline invertase 3 Assigned as NA-INV1 by Nemeth D and Hanumappa M (10/21/2010)" +Delta-COP GeneProduct :LOC_Os01g61710 "Delta coatamer " +SSII-2 GeneProduct :LOC_Os02g51070 "Also called ALK" +Terpene cyclases GeneProduct :LOC_Os04g27190 "" +MCM2 GeneProduct :LOC_Os11g29380 "" +Rab21 GeneProduct :LOC_Os11g26790 "ABA related water stress + cold stress" +CML18 GeneProduct :LOC_Os05g13580 "" +GF14c GeneProduct :LOC_Os08g33370 "" +UGP1 GeneProduct :LOC_Os09g38030 "" +FDH GeneProduct :LOC_Os02g57040 "Alcohol dehydrogenase class 3; Also called FALDH, GSH-FDH (Glutathione-dependent formaldehyde dehydrogenase)" +LOC_Os05g50190 GeneProduct :LOC_Os05g50190 "Protein Kinase-UniProt ID" +LOC_Os04g41910 GeneProduct :LOC_Os04g41910 "" +RIR 1b GeneProduct :LOC_Os05g48260 "" +CPL1 GeneProduct :LOC_Os07g10690 "Seed Shattering" +FBO10 GeneProduct :LOC_Os11g34460 "Adagio-like protein 3 Cytochrome P450" +OsCCP GeneProduct :LOC_Os12g08760 "Assigned as OsCCP by Nemeth D and Hanumappa M (10/21/2010) carboxyvinyl-carboxyphosphonate phosphorylmutase" +JA cmtr GeneProduct :LOC_Os06g22440 "Putative S-adenosyl-L-methionine Subtilisin N-terminal Region" +ISA2 GeneProduct :LOC_Os05g32710 "" +Bam 6 GeneProduct :LOC_Os09g39570 "" +PROLM28 GeneProduct :LOC_Os12g16890 "Prolamin precursor, protein also called PPROL 17 " +Pumilio GeneProduct :LOC_Os12g31000 "Leucine rich repeat" +IRT1 GeneProduct :LOC_Os03g46470 "" +Oligopeptide transporter 3 GeneProduct :LOC_Os03g54000 "Isp4-like " +MADS-box IL GeneProduct :LOC_Os02g54080 "" +ATP synthase GeneProduct :LOC_Os03g17070 "" +GluB-1A GeneProduct :LOC_Os02g15169 "UniProt ID: P14323" +MLA10 GeneProduct :LOC_Os11g16470 "Ankyrin repeat" +RPK-TMK1 precursor GeneProduct :LOC_Os04g58910 "receptor protein kinase TMK1 precursor" +MADS 2 GeneProduct :LOC_Os01g66030 "" +LOC_Os12g37570 GeneProduct :LOC_Os12g37570 "Protein Kinase-UniProt ID" +DIP1 GeneProduct :LOC_Os05g34070 "" +EBP89 GeneProduct :LOC_Os03g08460 "Also called EREBP1" +SUT2 GeneProduct :LOC_Os12g44380 "" +CycB1;1 GeneProduct :LOC_Os01g59120 "Seed Shattering" +SPP1 GeneProduct :LOC_Os01g27880 "sucrose-phosphatase 1 " +S-REP GeneProduct :LOC_Os04g47990 "" +bhlh113 GeneProduct :LOC_Os10g40740 "basic/helix-loop-helix 113" +APL1 GeneProduct :LOC_Os05g50380 "ADP-glucose Pyrophosphorylase large subunit 1 " +CTR1-like GeneProduct :LOC_Os09g39320 "Multitransmembrane protein" +DREB1B GeneProduct :LOC_Os09g35010 "" +RUBQ1 GeneProduct :LOC_Os02g06640 "Also called Polyubiquitin 6 Also given LOC_Os05g42424 which is not complete" +NADPH G-3-P dh GeneProduct :LOC_Os08g34210 "" +Sdr4 GeneProduct :LOC_Os07g39700 "" +Ring Finger GeneProduct :LOC_Os01g01390 "" +SSIIc GeneProduct :LOC_Os10g30156 "Also called ALK" +LOC_Os04g57020 GeneProduct :LOC_Os04g57020 "" +PSII-OEP33 GeneProduct :LOC_Os01g31690 "No symbol in gramene so OEP33 was assigned. 33kDa oxygen evolving protein of photosystem II" +LOC_Os04g53350 GeneProduct :LOC_Os04g53350 "Cooper 31122 ID" +CRINKLY4 GeneProduct :LOC_Os08g28710 "" +RAG-1 GeneProduct :LOC_Os09g16260 "RISBZ1 + RPBF activated the RAG-1 promoter greater than RPBF alone, though RISBZ1 did not independently affect promoter activity" +CR4 GeneProduct :LOC_Os03g43670 "homology with Crinkly4" +SSA1 GeneProduct :LOC_Os05g41970 "26 kDa alpha globulin" +TATC GeneProduct :LOC_Os01g31680 "" +DPE1 GeneProduct :LOC_Os07g43390 "" +LOC_Os02g53890 GeneProduct :LOC_Os02g53890 "" diff --git a/pathways/WP2199/WP2199.gpml b/pathways/WP2199/WP2199.gpml index 99bad7db5..6fdabdaef 100644 --- a/pathways/WP2199/WP2199.gpml +++ b/pathways/WP2199/WP2199.gpml @@ -1,5 +1,5 @@ - + The network features protein-protein interactions related to seed development in rice. Co-expression information for some genes known to be important for seed development is also shown. The Gene Basket contains a few genes/proteins that are known to be important for the process but for which interactions were unknown or intentionally left out when the network was created. Please go ahead and move them into the network if you find the correct interacting partner(s). @@ -678,7 +678,6 @@ complex 1 family protein-like (LYR family) 2 more IDs found on Gramene. Hence called 1, 2 and 3 to differentiate. LOC_Os06g27760=msrB-2, LOC_Os05g33510=msrB-3 (D Nemeth and M Hanumappa 08/17/2010). - Type your comment here e3b @@ -6018,49 +6017,6 @@ Also given LOC_Os05g42424 which is not complete - - 18308732 - PubMed - A novel NAC transcription factor, IDEF2, that recognizes the iron deficiency-responsive element 2 regulates the genes involved in iron homeostasis in plants. - J Biol Chem - 2008 - Ogo Y - Kobayashi T - Nakanishi Itai R - Nakanishi H - Kakei Y - Takahashi M - Toki S - Mori S - Nishizawa NK - - - 18723578 - PubMed - RACK1 functions in rice innate immunity by interacting with the Rac1 immune complex. - Plant Cell - 2008 - Nakashima A - Chen L - Thao NP - Fujiwara M - Wong HL - Kuwano M - Umemura K - Shirasu K - Kawasaki T - Shimamoto K - - - 8193305 - PubMed - Sequence and functional analyses of the rice gene homologous to the maize Vp1. - Plant Mol Biol - 1994 - Hattori T - Terada T - Hamasuna ST - 21037241 PubMed @@ -6070,32 +6026,91 @@ Also given LOC_Os05g42424 which is not complete Kawakatsu T Takaiwa F - - 9596641 + + 20567981 PubMed - 14-3-3 proteins are part of an abscisic acid-VIVIPAROUS1 (VP1) response complex in the Em promoter and interact with VP1 and EmBP1. - Plant Cell - 1998 - Schultz TF - Medina J - Hill A - Quatrano RS + Functional analysis of six drought-inducible promoters in transgenic rice plants throughout all stages of plant growth. + Planta + 2010 + Yi N + Kim YS + Jeong MH + Oh SJ + Jeong JS + Park SH + Jung H + Choi YD + Kim JK - - 18599581 + + 12947109 PubMed - Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. - Plant Cell - 2008 - Chen S - Yang Y - Shi W - Ji Q - He F - Zhang Z - Cheng Z - Liu X - Xu M + An interaction between a MYC protein and an EREBP protein is involved in transcriptional regulation of the rice Wx gene. + J Biol Chem + 2003 + Zhu Y + Cai XL + Wang ZY + Hong MM + + + 20974950 + PubMed + Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. + Proc Natl Acad Sci U S A + 2010 + Mao H + Sun S + Yao J + Wang C + Yu S + Xu C + Li X + Zhang Q + + + 19807881 + PubMed + Inactivation of the CTD phosphatase-like gene OsCPL1 enhances the development of the abscission layer and seed shattering in rice. + Plant J + 2010 + Ji H + Kim SR + Kim YH + Kim H + Eun MY + Jin ID + Cha YS + Yun DW + Ahn BO + Lee MC + Lee GS + Yoon UH + Lee JS + Lee YH + Suh SC + Jiang W + Yang JI + Jin P + McCouch SR + An G + Koh HJ + + + 18826428 + PubMed + Contribution of salicylic acid glucosyltransferase, OsSGT1, to chemically induced disease resistance in rice plants. + Plant J + 2009 + Umemura K + Satou J + Iwata M + Uozumi N + Koga J + Kawano T + Koshiba T + Anzai H + Mitomi M 20305271 @@ -6111,106 +6126,108 @@ Also given LOC_Os05g42424 which is not complete Yoshida M Kitamura S - - 11910009 + + 15220467 PubMed - Rice SPK, a calmodulin-like domain protein kinase, is required for storage product accumulation during seed development: phosphorylation of sucrose synthase is a possible factor. - Plant Cell - 2002 - Asano T - Kunieda N - Omura Y - Ibe H + Down-regulation of metallothionein, a reactive oxygen scavenger, by the small GTPase OsRac1 in rice. + Plant Physiol + 2004 + Wong HL + Sakamoto T Kawasaki T - Takano M - Sato M - Furuhashi H - Mujin T - Takaiwa F - Wu Cy CY - Tada Y - Satozawa T - Sakamoto M - Shimada H + Umemura K + Shimamoto K - - 17297616 + + 19052152 PubMed - Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.). - Plant Cell Rep - 2007 - Ryoo N - Yu C - Park CS - Baik MY - Park IM - Cho MH - Bhoo SH + Rice aldehyde dehydrogenase7 is needed for seed maturation and viability. + Plant Physiol + 2009 + Shin JH + Kim SR An G - Hahn TR - Jeon JS - - 20713616 + + 16152656 PubMed - Coexpression analysis identifies Rice Starch Regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator. - Plant Physiol - 2010 - Fu FF - Xue HW + Proteomic analysis of rice embryo: an approach for investigating Galpha protein-regulated proteins. + Proteomics + 2005 + Komatsu S + Abbasi F + Kobori E + Fujisawa Y + Kato H + Iwasaki Y - - 20632034 + + 15976269 PubMed - The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. - Mol Genet Genomics - 2010 - Takasaki H - Maruyama K - Kidokoro S - Ito Y - Fujita Y - Shinozaki K - Yamaguchi-Shinozaki K - Nakashima K + Cytokinin oxidase regulates rice grain production. + Science + 2005 + Ashikari M + Sakakibara H + Lin S + Yamamoto T + Takashi T + Nishimura A + Angeles ER + Qian Q + Kitano H + Matsuoka M - - 19506305 + + 20889913 PubMed - Evolutionary history of GS3, a gene conferring grain length in rice. - Genetics - 2009 - Takano-Kai N - Jiang H - Kubo T - Sweeney M - Matsumoto T - Kanamori H - Padhukasahasram B - Bustamante C - Yoshimura A - Doi K - McCouch S + A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. + Plant Cell + 2010 + She KC + Kusano H + Koizumi K + Yamakawa H + Hakata M + Imamura T + Fukuda M + Naito N + Tsurumaki Y + Yaeshima M + Tsuge T + Matsumoto K + Kudoh M + Itoh E + Kikuchi S + Kishimoto N + Yazaki J + Ando T + Yano M + Aoyama T + Sasaki T + Satoh H + Shimada H - - 18820698 + + 8193305 PubMed - Control of rice grain-filling and yield by a gene with a potential signature of domestication. - Nat Genet + Sequence and functional analyses of the rice gene homologous to the maize Vp1. + Plant Mol Biol + 1994 + Hattori T + Terada T + Hamasuna ST + + + 18755073 + PubMed + Identification and characterization of a rice MCM2 homologue required for DNA replication. + BMB Rep 2008 - Wang E - Wang J - Zhu X - Hao W - Wang L - Li Q - Zhang L - He W - Lu B - Lin H - Ma H - Zhang G - He Z + Cho JH + Kim HB + Kim HS + Choi SB 17339651 @@ -6226,84 +6243,59 @@ Also given LOC_Os05g42424 which is not complete Hell R Sauter M - - 17587305 - PubMed - Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. - Plant J - 2007 - Nakashima K - Tran LS - Van Nguyen D - Fujita M - Maruyama K - Todaka D - Ito Y - Hayashi N - Shinozaki K - Yamaguchi-Shinozaki K - - - 10987556 - PubMed - The cell cycle genes cycA1;1 and cdc2Os-3 are coordinately regulated by gibberellin in planta. - Planta - 2000 - Fabian T - Lorbiecke R - Umeda M - Sauter M - - - 20829346 + + 24280312 PubMed - Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L. - Mol Biol Evol - 2011 - Yu G - Olsen KM - Schaal BA + WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks + Rice 2013, 6:14 doi:10.1186/1939-8433-6-14 (http://www.thericejournal.com/content/6/1/14/) + 2013 + Mamatha Hanumappa, Justin Preece, Justin Elser, Denise Nemeth, Gina Bono, Kenny Wu, Pankaj Jaiswal - - 20490919 + + signaling pathway + PW:0000003 + Pathway Ontology + + + 19593540 PubMed - Analysis of the Wsi18, a stress-inducible promoter that is active in the whole grain of transgenic rice. - Transgenic Res - 2011 - Yi N - Oh SJ - Kim YS - Jang HJ - Park SH - Jeong JS - Song SI - Choi YD - Kim JK + Comparison of the starch synthesis genes between maize and rice: copies, chromosome location and expression divergence. + Theor Appl Genet + 2009 + Yan HB + Pan XX + Jiang HW + Wu GJ - - 15356337 + + 19682292 PubMed - A rice antisense SPK transformant that lacks the accumulation of seed storage substances shows no correlation between sucrose concentration in phloem sap and demand for carbon sources in the sink organs. - Plant Cell Physiol - 2004 - Shimada H - Koishihara H - Saito Y - Arashima Y - Furukawa T - Hayashi H + Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling. + Plant Cell Environ + 2009 + Bi YM + Kant S + Clarke J + Gidda S + Ming F + Xu J + Rochon A + Shelp BJ + Hao L + Zhao R + Mullen RT + Zhu T + Rothstein SJ - - 19921249 + + 19266169 PubMed - The expression of Orysa;CycB1;1 is essential for endosperm formation and causes embryo enlargement in rice. - Planta - 2010 - Guo J - Wang F - Song J - Sun W - Zhang XS + Characterization of OsIAA1 gene, a member of rice Aux/IAA family involved in auxin and brassinosteroid hormone responses and plant morphogenesis. + Plant Mol Biol + 2009 + Song Y + You J + Xiong L 19321714 @@ -6320,142 +6312,68 @@ Also given LOC_Os05g42424 which is not complete Wobus U Weschke W - - 20220098 - PubMed - Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. - Proc Natl Acad Sci U S A - 2010 - Sugimoto K - Takeuchi Y - Ebana K - Miyao A - Hirochika H - Hara N - Ishiyama K - Kobayashi M - Ban Y - Hattori T - Yano M - - - 19490115 + + 9596641 PubMed - Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. - FEBS J - 2009 - Jain M - Khurana JP + 14-3-3 proteins are part of an abscisic acid-VIVIPAROUS1 (VP1) response complex in the Em promoter and interact with VP1 and EmBP1. + Plant Cell + 1998 + Schultz TF + Medina J + Hill A + Quatrano RS - - 15759120 + + 19015668 PubMed - Molecular cloning and expression analysis of the cell-wall invertase gene family in rice (Oryza sativa L.). - Plant Cell Rep - 2005 - Cho JI - Lee SK - Ko S - Kim HK - Jun SH - Lee YH - Bhoo SH - Lee KW - An G - Hahn TR - Jeon JS + Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. + Cell Res + 2008 + Weng J + Gu S + Wan X + Gao H + Guo T + Su N + Lei C + Zhang X + Cheng Z + Guo X + Wang J + Jiang L + Zhai H + Wan J - - 15220467 + + 20490919 PubMed - Down-regulation of metallothionein, a reactive oxygen scavenger, by the small GTPase OsRac1 in rice. - Plant Physiol - 2004 - Wong HL - Sakamoto T - Kawasaki T - Umemura K - Shimamoto K - - - 18713381 - PubMed - Cell-wall invertases from rice are differentially expressed in Caryopsis during the grain filling stage. - J Integr Plant Biol - 2008 - Wang YQ - Wei XL - Xu HL - Chai CL - Meng K - Zhai HL - Sun AJ - Peng YG - Wu B - Xiao GF - Zhu Z - - - 15976269 - PubMed - Cytokinin oxidase regulates rice grain production. - Science - 2005 - Ashikari M - Sakakibara H - Lin S - Yamamoto T - Takashi T - Nishimura A - Angeles ER - Qian Q - Kitano H - Matsuoka M - - - 19266169 - PubMed - Characterization of OsIAA1 gene, a member of rice Aux/IAA family involved in auxin and brassinosteroid hormone responses and plant morphogenesis. - Plant Mol Biol - 2009 - Song Y - You J - Xiong L - - - 12684538 - PubMed - A network of rice genes associated with stress response and seed development. - Proc Natl Acad Sci U S A - 2003 - Cooper B - Clarke JD - Budworth P - Kreps J - Hutchison D - Park S - Guimil S - Dunn M - Luginbühl P - Ellero C - Goff SA - Glazebrook J + Analysis of the Wsi18, a stress-inducible promoter that is active in the whole grain of transgenic rice. + Transgenic Res + 2011 + Yi N + Oh SJ + Kim YS + Jang HJ + Park SH + Jeong JS + Song SI + Choi YD + Kim JK - - 18156216 + + 20460361 PubMed - RAR1 and HSP90 form a complex with Rac/Rop GTPase and function in innate-immune responses in rice. - Plant Cell - 2007 - Thao NP - Chen L - Nakashima A - Hara S - Umemura K - Takahashi A - Shirasu K - Kawasaki T - Shimamoto K + Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice. + J Exp Bot + 2010 + Sun SJ + Guo SQ + Yang X + Bao YM + Tang HJ + Sun H + Huang J + Zhang HS 20416079 @@ -6475,149 +6393,108 @@ Also given LOC_Os05g42424 which is not complete Wang W He Z - - 18826428 + + 16786297 PubMed - Contribution of salicylic acid glucosyltransferase, OsSGT1, to chemically induced disease resistance in rice plants. - Plant J - 2009 - Umemura K - Satou J - Iwata M - Uozumi N - Koga J - Kawano T - Koshiba T - Anzai H - Mitomi M + OsEIL1, a rice homolog of the Arabidopsis EIN3 regulates the ethylene response as a positive component. + Plant Mol Biol + 2006 + Mao C + Wang S + Jia Q + Wu P - - 19429605 + + 16667159 PubMed - Overexpression of the transcription factor AP37 in rice improves grain yield under drought conditions. + Effects of cold-treatment on protein synthesis and mRNA levels in rice leaves. Plant Physiol - 2009 - Oh SJ - Kim YS - Kwon CW - Park HK - Jeong JS - Kim JK + 1989 + Hahn M + Walbot V - - 19933315 + + 17426956 PubMed - The syncytium-specific expression of the Orysa;KRP3 CDK inhibitor: implication of its involvement in the cell cycle control in the rice (Oryza sativa L.) syncytial endosperm. - J Exp Bot - 2010 - Mizutani M - Naganuma T - Tsutsumi K - Saitoh Y + Over-expression of a LEA gene in rice improves drought resistance under the field conditions. + Theor Appl Genet + 2007 + Xiao B + Huang Y + Tang N + Xiong L - - 14733924 + + 15356337 PubMed - Characterization of Rad6 from a higher plant, rice (Oryza sativa L.) and its interaction with Sgt1, a subunit of the SCF ubiquitin ligase complex. - Biochem Biophys Res Commun + A rice antisense SPK transformant that lacks the accumulation of seed storage substances shows no correlation between sucrose concentration in phloem sap and demand for carbon sources in the sink organs. + Plant Cell Physiol 2004 - Yamamoto T - Mori Y - Ishibashi T - Uchiyama Y - Sakaguchi N + Shimada H + Koishihara H + Saito Y + Arashima Y Furukawa T - Hashimoto J - Kimura S - Sakaguchi K + Hayashi H - - 19015668 + + 16953433 PubMed - Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. - Cell Res - 2008 - Weng J - Gu S - Wan X - Gao H - Guo T - Su N - Lei C - Zhang X - Cheng Z - Guo X - Wang J - Jiang L - Zhai H - Wan J + Structural and enzymatic characterization of the isoamylase1 homo-oligomer and the isoamylase1-isoamylase2 hetero-oligomer from rice endosperm. + Planta + 2006 + Utsumi Y + Nakamura Y - - 20889913 + + 15047897 PubMed - A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. - Plant Cell - 2010 - She KC - Kusano H - Koizumi K - Yamakawa H - Hakata M - Imamura T - Fukuda M - Naito N - Tsurumaki Y - Yaeshima M - Tsuge T - Matsumoto K - Kudoh M - Itoh E - Kikuchi S - Kishimoto N - Yazaki J - Ando T - Yano M - Aoyama T - Sasaki T - Satoh H - Shimada H + A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. + Plant Physiol + 2004 + Zhang ZL + Xie Z + Zou X + Casaretto J + Ho TH + Shen QJ - - 10417713 - PubMed - RNA maturation of the rice SPK gene may involve trans-splicing. - Plant J - 1999 - Kawasaki T - Okumura S - Kishimoto N - Shimada H - Higo K - Ichikawa N - - - 12947109 + + 18840300 PubMed - An interaction between a MYC protein and an EREBP protein is involved in transcriptional regulation of the rice Wx gene. - J Biol Chem - 2003 - Zhu Y - Cai XL - Wang ZY - Hong MM + RNAi-directed downregulation of OsBADH2 results in aroma (2-acetyl-1-pyrroline) production in rice (Oryza sativa L.). + BMC Plant Biol + 2008 + Niu X + Tang W + Huang W + Ren G + Wang Q + Luo D + Xiao Y + Yang S + Wang F + Lu BR + Gao F + Lu T + Liu Y - - 17579813 + + 17297616 PubMed - Du1, encoding a novel Prp1 protein, regulates starch biosynthesis through affecting the splicing of Wxb pre-mRNAs in rice (Oryza sativa L.). - Plant Mol Biol + Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.). + Plant Cell Rep 2007 - Zeng D - Yan M - Wang Y - Liu X - Qian Q - Li J + Ryoo N + Yu C + Park CS + Baik MY + Park IM + Cho MH + Bhoo SH + An G + Hahn TR + Jeon JS 18025467 @@ -6633,70 +6510,138 @@ Also given LOC_Os05g42424 which is not complete Mori S Nishizawa NK - - 12783325 + + 10805599 PubMed - Interaction between proliferating cell nuclear antigen and JUN-activation-domain-binding protein 1 in the meristem of rice, Oryza sativa L. - Planta - 2003 - Yamamoto T - Kimura S - Mori Y - Uchiyama Y - Ishibashi T - Hashimoto J - Sakaguchi K + Hormonal cross-talk between auxin and ethylene differentially regulates the expression of two members of the 1-aminocyclopropane-1-carboxylate oxidase gene family in rice (Oryza sativa L.). + Plant Cell Physiol + 2000 + Chae HS + Cho YG + Park MY + Lee MC + Eun MY + Kang BG + Kim WT - - 16667159 + + 19737364 PubMed - Effects of cold-treatment on protein synthesis and mRNA levels in rice leaves. - Plant Physiol - 1989 - Hahn M - Walbot V + The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes. + Plant J + 2009 + Kobayashi T + Itai RN + Ogo Y + Kakei Y + Nakanishi H + Takahashi M + Nishizawa NK - - 15232694 + + 18723578 PubMed - A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). + RACK1 functions in rice innate immunity by interacting with the Rac1 immune complex. + Plant Cell + 2008 + Nakashima A + Chen L + Thao NP + Fujiwara M + Wong HL + Kuwano M + Umemura K + Shirasu K + Kawasaki T + Shimamoto K + + + 10987556 + PubMed + The cell cycle genes cycA1;1 and cdc2Os-3 are coordinately regulated by gibberellin in planta. Planta - 2004 + 2000 + Fabian T + Lorbiecke R + Umeda M + Sauter M + + + 20220098 + PubMed + Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice. + Proc Natl Acad Sci U S A + 2010 + Sugimoto K + Takeuchi Y + Ebana K + Miyao A + Hirochika H + Hara N + Ishiyama K + Kobayashi M + Ban Y + Hattori T + Yano M + + + 20478538 + PubMed + Activation of a Rac GTPase by the NLR family disease resistance protein Pit plays a critical role in rice innate immunity. + Cell Host Microbe + 2010 + Kawano Y + Akamatsu A + Hayashi K + Housen Y + Okuda J + Yao A + Nakashima A + Takahashi H + Yoshida H + Wong HL + Kawasaki T + Shimamoto K + + + 16275672 + PubMed + Expression profiling of genes involved in starch synthesis in sink and source organs of rice. + J Exp Bot + 2005 + Ohdan T + Francisco PB Jr + Sawada T Hirose T Terao T + Satoh H + Nakamura Y - - 16896230 + + 10417713 PubMed - Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. - Plant Physiol - 2006 - Li X - Duan X - Jiang H - Sun Y - Tang Y - Yuan Z - Guo J - Liang W - Chen L - Yin J - Ma H - Wang J - Zhang D + RNA maturation of the rice SPK gene may involve trans-splicing. + Plant J + 1999 + Kawasaki T + Okumura S + Kishimoto N + Shimada H + Higo K + Ichikawa N - - 16623886 + + 19429605 PubMed - Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. - Plant J - 2006 - Xie Z - Zhang ZL - Zou X - Yang G - Komatsu S - Shen QJ + Overexpression of the transcription factor AP37 in rice improves grain yield under drought conditions. + Plant Physiol + 2009 + Oh SJ + Kim YS + Kwon CW + Park HK + Jeong JS + Kim JK 17604002 @@ -6710,96 +6655,165 @@ Also given LOC_Os05g42424 which is not complete Zhang F Chen F - - 17384160 + + 18156216 PubMed - Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. - Plant Physiol + RAR1 and HSP90 form a complex with Rac/Rop GTPase and function in innate-immune responses in rice. + Plant Cell 2007 - Yamakawa H - Hirose T - Kuroda M - Yamaguchi T + Thao NP + Chen L + Nakashima A + Hara S + Umemura K + Takahashi A + Shirasu K + Kawasaki T + Shimamoto K - - 20335401 + + 14733924 PubMed - Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. - Plant Physiol - 2010 - Jeong JS - Kim YS - Baek KH - Jung H - Ha SH - Do Choi Y - Kim M - Reuzeau C - Kim JK + Characterization of Rad6 from a higher plant, rice (Oryza sativa L.) and its interaction with Sgt1, a subunit of the SCF ubiquitin ligase complex. + Biochem Biophys Res Commun + 2004 + Yamamoto T + Mori Y + Ishibashi T + Uchiyama Y + Sakaguchi N + Furukawa T + Hashimoto J + Kimura S + Sakaguchi K - - 19682292 + + 17579813 PubMed - Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling. - Plant Cell Environ - 2009 - Bi YM - Kant S - Clarke J - Gidda S - Ming F - Xu J - Rochon A - Shelp BJ - Hao L - Zhao R - Mullen RT - Zhu T - Rothstein SJ + Du1, encoding a novel Prp1 protein, regulates starch biosynthesis through affecting the splicing of Wxb pre-mRNAs in rice (Oryza sativa L.). + Plant Mol Biol + 2007 + Zeng D + Yan M + Wang Y + Liu X + Qian Q + Li J - - 18257679 + + 17587305 PubMed - OsRAR1 and OsSGT1 physically interact and function in rice basal disease resistance. - Mol Plant Microbe Interact + Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice. + Plant J + 2007 + Nakashima K + Tran LS + Van Nguyen D + Fujita M + Maruyama K + Todaka D + Ito Y + Hayashi N + Shinozaki K + Yamaguchi-Shinozaki K + + + 12783325 + PubMed + Interaction between proliferating cell nuclear antigen and JUN-activation-domain-binding protein 1 in the meristem of rice, Oryza sativa L. + Planta + 2003 + Yamamoto T + Kimura S + Mori Y + Uchiyama Y + Ishibashi T + Hashimoto J + Sakaguchi K + + + 18713381 + PubMed + Cell-wall invertases from rice are differentially expressed in Caryopsis during the grain filling stage. + J Integr Plant Biol 2008 - Wang Y - Gao M - Li Q - Wang L + Wang YQ + Wei XL + Xu HL + Chai CL + Meng K + Zhai HL + Sun AJ + Peng YG + Wu B + Xiao GF + Zhu Z + + + 20829346 + PubMed + Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L. + Mol Biol Evol + 2011 + Yu G + Olsen KM + Schaal BA + + + 20713616 + PubMed + Coexpression analysis identifies Rice Starch Regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator. + Plant Physiol + 2010 + Fu FF + Xue HW + + + 18820698 + PubMed + Control of rice grain-filling and yield by a gene with a potential signature of domestication. + Nat Genet + 2008 + Wang E Wang J - Jeon JS - Qu N - Zhang Y + Zhu X + Hao W + Wang L + Li Q + Zhang L + He W + Lu B + Lin H + Ma H + Zhang G He Z - - 16786297 + + 17376611 PubMed - OsEIL1, a rice homolog of the Arabidopsis EIN3 regulates the ethylene response as a positive component. - Plant Mol Biol - 2006 - Mao C - Wang S - Jia Q - Wu P + Characterization of a lipoate-protein ligase A gene of rice (Oryza sativa L.). + Gene + 2007 + Kang SG + Jeong HK + Lee E + Natarajan S - - 17426956 + + 20632034 PubMed - Over-expression of a LEA gene in rice improves drought resistance under the field conditions. - Theor Appl Genet - 2007 - Xiao B - Huang Y - Tang N - Xiong L + The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice. + Mol Genet Genomics + 2010 + Takasaki H + Maruyama K + Kidokoro S + Ito Y + Fujita Y + Shinozaki K + Yamaguchi-Shinozaki K + Nakashima K - - plant cell - CL:0000610 - Cell Type - 17559517 PubMed @@ -6814,16 +6828,6 @@ Also given LOC_Os05g42424 which is not complete Mori S Nishizawa NK - - 19052152 - PubMed - Rice aldehyde dehydrogenase7 is needed for seed maturation and viability. - Plant Physiol - 2009 - Shin JH - Kim SR - An G - 15806324 PubMed @@ -6840,114 +6844,146 @@ Also given LOC_Os05g42424 which is not complete Kimura S Sakaguchi K - - 16953433 + + 16896230 PubMed - Structural and enzymatic characterization of the isoamylase1 homo-oligomer and the isoamylase1-isoamylase2 hetero-oligomer from rice endosperm. - Planta + Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis. + Plant Physiol 2006 - Utsumi Y - Nakamura Y + Li X + Duan X + Jiang H + Sun Y + Tang Y + Yuan Z + Guo J + Liang W + Chen L + Yin J + Ma H + Wang J + Zhang D - - 15047897 + + 16798940 PubMed - A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells. + Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes. Plant Physiol - 2004 - Zhang ZL - Xie Z - Zou X - Casaretto J - Ho TH - Shen QJ + 2006 + Yamamoto MP + Onodera Y + Touno SM + Takaiwa F - - signaling pathway - PW:0000003 - Pathway Ontology - - - 20478538 + + 19933315 PubMed - Activation of a Rac GTPase by the NLR family disease resistance protein Pit plays a critical role in rice innate immunity. - Cell Host Microbe + The syncytium-specific expression of the Orysa;KRP3 CDK inhibitor: implication of its involvement in the cell cycle control in the rice (Oryza sativa L.) syncytial endosperm. + J Exp Bot 2010 - Kawano Y - Akamatsu A - Hayashi K - Housen Y - Okuda J - Yao A - Nakashima A - Takahashi H - Yoshida H - Wong HL - Kawasaki T - Shimamoto K + Mizutani M + Naganuma T + Tsutsumi K + Saitoh Y - - 19737364 + + 16623886 PubMed - The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes. + Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells. + Plant J + 2006 + Xie Z + Zhang ZL + Zou X + Yang G + Komatsu S + Shen QJ + + + 19473328 + PubMed + Compensation and interaction between RISBZ1 and RPBF during grain filling in rice. Plant J 2009 - Kobayashi T - Itai RN - Ogo Y - Kakei Y - Nakanishi H - Takahashi M - Nishizawa NK + Kawakatsu T + Yamamoto MP + Touno SM + Yasuda H + Takaiwa F - - 20974950 + + 19490115 PubMed - Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. - Proc Natl Acad Sci U S A - 2010 - Mao H - Sun S - Yao J - Wang C - Yu S - Xu C - Li X - Zhang Q + Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. + FEBS J + 2009 + Jain M + Khurana JP - - 10805599 + + 19506305 PubMed - Hormonal cross-talk between auxin and ethylene differentially regulates the expression of two members of the 1-aminocyclopropane-1-carboxylate oxidase gene family in rice (Oryza sativa L.). - Plant Cell Physiol - 2000 - Chae HS - Cho YG - Park MY - Lee MC - Eun MY - Kang BG - Kim WT + Evolutionary history of GS3, a gene conferring grain length in rice. + Genetics + 2009 + Takano-Kai N + Jiang H + Kubo T + Sweeney M + Matsumoto T + Kanamori H + Padhukasahasram B + Bustamante C + Yoshimura A + Doi K + McCouch S - - 8940135 + + 18308732 PubMed - Characterization of three rice basic/leucine zipper factors, including two inhibitors of EmBP-1 DNA binding activity. + A novel NAC transcription factor, IDEF2, that recognizes the iron deficiency-responsive element 2 regulates the genes involved in iron homeostasis in plants. J Biol Chem - 1996 - Nantel A - Quatrano RS + 2008 + Ogo Y + Kobayashi T + Nakanishi Itai R + Nakanishi H + Kakei Y + Takahashi M + Toki S + Mori S + Nishizawa NK - - 16436304 + + 15891897 PubMed - Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress. - J Plant Physiol - 2006 - Cao Y - Song F - Goodman RM - Zheng Z + Identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins. + Planta + 2005 + Kasai K + Kanno T + Akita M + Ikejiri-Kanno Y + Wakasa K + Tozawa Y + + + 15759120 + PubMed + Molecular cloning and expression analysis of the cell-wall invertase gene family in rice (Oryza sativa L.). + Plant Cell Rep + 2005 + Cho JI + Lee SK + Ko S + Kim HK + Jun SH + Lee YH + Bhoo SH + Lee KW + An G + Hahn TR + Jeon JS 18454147 @@ -6967,6 +7003,21 @@ Also given LOC_Os05g42424 which is not complete Li X Zhang Q + + 18315698 + PubMed + Abscisic acid regulates gene expression in cortical fiber cells and silica cells of rice shoots. + New Phytol + 2008 + Shobbar ZS + Oane R + Gamuyao R + De Palma J + Malboobi MA + Karimzadeh G + Javaran MJ + Bennett J + 17406793 PubMed @@ -6987,217 +7038,165 @@ Also given LOC_Os05g42424 which is not complete Okita TW Jeon JS - - 16152656 + + 18257679 PubMed - Proteomic analysis of rice embryo: an approach for investigating Galpha protein-regulated proteins. - Proteomics - 2005 - Komatsu S - Abbasi F - Kobori E - Fujisawa Y - Kato H - Iwasaki Y + OsRAR1 and OsSGT1 physically interact and function in rice basal disease resistance. + Mol Plant Microbe Interact + 2008 + Wang Y + Gao M + Li Q + Wang L + Wang J + Jeon JS + Qu N + Zhang Y + He Z - - 19593540 + + 15232694 PubMed - Comparison of the starch synthesis genes between maize and rice: copies, chromosome location and expression divergence. - Theor Appl Genet - 2009 - Yan HB - Pan XX - Jiang HW - Wu GJ + A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). + Planta + 2004 + Hirose T + Terao T - - 17376611 + + 18599581 PubMed - Characterization of a lipoate-protein ligase A gene of rice (Oryza sativa L.). - Gene - 2007 - Kang SG - Jeong HK - Lee E - Natarajan S + Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance. + Plant Cell + 2008 + Chen S + Yang Y + Shi W + Ji Q + He F + Zhang Z + Cheng Z + Liu X + Xu M - - 24280312 + + 8940135 PubMed - WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks - Rice 2013, 6:14 doi:10.1186/1939-8433-6-14 (http://www.thericejournal.com/content/6/1/14/) - 2013 - Mamatha Hanumappa, Justin Preece, Justin Elser, Denise Nemeth, Gina Bono, Kenny Wu, Pankaj Jaiswal + Characterization of three rice basic/leucine zipper factors, including two inhibitors of EmBP-1 DNA binding activity. + J Biol Chem + 1996 + Nantel A + Quatrano RS - - 20460361 + + 17384160 PubMed - Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice. - J Exp Bot - 2010 - Sun SJ - Guo SQ - Yang X - Bao YM - Tang HJ - Sun H - Huang J - Zhang HS + Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray. + Plant Physiol + 2007 + Yamakawa H + Hirose T + Kuroda M + Yamaguchi T - - 18315698 + + 19921249 PubMed - Abscisic acid regulates gene expression in cortical fiber cells and silica cells of rice shoots. - New Phytol - 2008 - Shobbar ZS - Oane R - Gamuyao R - De Palma J - Malboobi MA - Karimzadeh G - Javaran MJ - Bennett J + The expression of Orysa;CycB1;1 is essential for endosperm formation and causes embryo enlargement in rice. + Planta + 2010 + Guo J + Wang F + Song J + Sun W + Zhang XS - - 17640358 + + plant cell + CL:0000610 + Cell Type + + + 12684538 PubMed - MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. - BMC Genomics - 2007 - Arora R - Agarwal P - Ray S - Singh AK - Singh VP - Tyagi AK - Kapoor S + A network of rice genes associated with stress response and seed development. + Proc Natl Acad Sci U S A + 2003 + Cooper B + Clarke JD + Budworth P + Kreps J + Hutchison D + Park S + Guimil S + Dunn M + Luginbühl P + Ellero C + Goff SA + Glazebrook J - - 20567981 + + 20335401 PubMed - Functional analysis of six drought-inducible promoters in transgenic rice plants throughout all stages of plant growth. - Planta + Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. + Plant Physiol 2010 - Yi N - Kim YS - Jeong MH - Oh SJ Jeong JS - Park SH + Kim YS + Baek KH Jung H - Choi YD + Ha SH + Do Choi Y + Kim M + Reuzeau C Kim JK - - 16798940 + + 16436304 PubMed - Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes. - Plant Physiol + Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress. + J Plant Physiol 2006 - Yamamoto MP - Onodera Y - Touno SM - Takaiwa F - - - 16275672 - PubMed - Expression profiling of genes involved in starch synthesis in sink and source organs of rice. - J Exp Bot - 2005 - Ohdan T - Francisco PB Jr - Sawada T - Hirose T - Terao T - Satoh H - Nakamura Y - - - 18755073 - PubMed - Identification and characterization of a rice MCM2 homologue required for DNA replication. - BMB Rep - 2008 - Cho JH - Kim HB - Kim HS - Choi SB - - - 15891897 - PubMed - Identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins. - Planta - 2005 - Kasai K - Kanno T - Akita M - Ikejiri-Kanno Y - Wakasa K - Tozawa Y - - - 18840300 - PubMed - RNAi-directed downregulation of OsBADH2 results in aroma (2-acetyl-1-pyrroline) production in rice (Oryza sativa L.). - BMC Plant Biol - 2008 - Niu X - Tang W - Huang W - Ren G - Wang Q - Luo D - Xiao Y - Yang S - Wang F - Lu BR - Gao F - Lu T - Liu Y + Cao Y + Song F + Goodman RM + Zheng Z - - 19473328 + + 11910009 PubMed - Compensation and interaction between RISBZ1 and RPBF during grain filling in rice. - Plant J - 2009 - Kawakatsu T - Yamamoto MP - Touno SM - Yasuda H + Rice SPK, a calmodulin-like domain protein kinase, is required for storage product accumulation during seed development: phosphorylation of sucrose synthase is a possible factor. + Plant Cell + 2002 + Asano T + Kunieda N + Omura Y + Ibe H + Kawasaki T + Takano M + Sato M + Furuhashi H + Mujin T Takaiwa F + Wu Cy CY + Tada Y + Satozawa T + Sakamoto M + Shimada H - - 19807881 + + 17640358 PubMed - Inactivation of the CTD phosphatase-like gene OsCPL1 enhances the development of the abscission layer and seed shattering in rice. - Plant J - 2010 - Ji H - Kim SR - Kim YH - Kim H - Eun MY - Jin ID - Cha YS - Yun DW - Ahn BO - Lee MC - Lee GS - Yoon UH - Lee JS - Lee YH - Suh SC - Jiang W - Yang JI - Jin P - McCouch SR - An G - Koh HJ + MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress. + BMC Genomics + 2007 + Arora R + Agarwal P + Ray S + Singh AK + Singh VP + Tyagi AK + Kapoor S diff --git a/pathways/WP2199/WP2199.json b/pathways/WP2199/WP2199.json index 832bfd392..d7948f054 100644 --- a/pathways/WP2199/WP2199.json +++ b/pathways/WP2199/WP2199.json @@ -10961,7 +10961,8 @@ "Rice Ensembl Gene:LOC_Os01g63290", "GeneProduct", "CompactIdentifier::LOC_Os01g63290", - "PHT4;3" + "PHT4;3", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -11288,9 +11289,6 @@ "comments": [ { "content": "2 more IDs found on Gramene. Hence called 1, 2 and 3 to differentiate. LOC_Os06g27760=msrB-2, LOC_Os05g33510=msrB-3 (D Nemeth and M Hanumappa 08/17/2010)." - }, - { - "content": "Type your comment here" } ], "drawAs": "rect", @@ -13270,7 +13268,8 @@ "Rice Ensembl Gene:LOC_Os02g02550", "GeneProduct", "CompactIdentifier:GeneProduct", - "UGP" + "UGP", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -26387,7 +26386,8 @@ "Rice Ensembl Gene:LOC_Os02g02560", "GeneProduct", "CompactIdentifier:GeneProduct", - "UGP2" + "UGP2", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -26475,7 +26475,8 @@ "Rice Ensembl Gene:LOC_Os06g43590", "GeneProduct", "CompactIdentifier:GeneProduct", - "SAL1" + "SAL1", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -27915,7 +27916,8 @@ "Rice Ensembl Gene:LOC_Os03g55090", "GeneProduct", "CompactIdentifier:GeneProduct", - "PHOL" + "PHOL", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -36830,7 +36832,8 @@ "Rice Ensembl Gene:LOC_Os09g38030", "GeneProduct", "CompactIdentifier:GeneProduct", - "UGP1" + "UGP1", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -50024,7 +50027,7 @@ "id": "publicationXrefa10", "source": "Plant J", "standardName": "Compensation and interaction between RISBZ1 and RPBF during grain filling in rice.", - "textContent": "63", + "textContent": "61", "type": [ "PublicationXref", "PubMed:19473328" @@ -50075,7 +50078,7 @@ "id": "publicationXrefa18", "source": "J Plant Res", "standardName": "Interaction between proliferating cell nuclear antigen (PCNA) and a DnaJ induced by DNA damage.", - "textContent": "19", + "textContent": "20", "type": [ "PublicationXref", "PubMed:15806324" @@ -50128,7 +50131,7 @@ "id": "publicationXrefa55", "source": "Proteomics", "standardName": "Proteomic analysis of rice embryo: an approach for investigating Galpha protein-regulated proteins.", - "textContent": "20", + "textContent": "17", "type": [ "PublicationXref", "PubMed:16152656" @@ -50171,7 +50174,7 @@ "id": "publicationXrefa5f", "source": "Planta", "standardName": "Functional analysis of six drought-inducible promoters in transgenic rice plants throughout all stages of plant growth.", - "textContent": "77", + "textContent": "65", "type": [ "PublicationXref", "PubMed:20567981" @@ -50196,7 +50199,7 @@ "id": "publicationXrefa71", "source": "Biochem Biophys Res Commun", "standardName": "Characterization of Rad6 from a higher plant, rice (Oryza sativa L.) and its interaction with Sgt1, a subunit of the SCF ubiquitin ligase complex.", - "textContent": "14", + "textContent": "15", "type": [ "PublicationXref", "PubMed:14733924" @@ -50216,7 +50219,7 @@ "id": "publicationXrefa87", "source": "J Plant Physiol", "standardName": "Molecular characterization of four rice genes encoding ethylene-responsive transcriptional factors and their expressions in response to biotic and abiotic stress.", - "textContent": "27", + "textContent": "28", "type": [ "PublicationXref", "PubMed:16436304" @@ -50241,7 +50244,7 @@ "id": "publicationXrefaa5", "source": "J Biol Chem", "standardName": "A novel NAC transcription factor, IDEF2, that recognizes the iron deficiency-responsive element 2 regulates the genes involved in iron homeostasis in plants.", - "textContent": "42", + "textContent": "48", "type": [ "PublicationXref", "PubMed:18308732" @@ -50262,7 +50265,7 @@ "id": "publicationXrefad9", "source": "Planta", "standardName": "The expression of Orysa;CycB1;1 is essential for endosperm formation and causes embryo enlargement in rice.", - "textContent": "68", + "textContent": "77", "type": [ "PublicationXref", "PubMed:19921249" @@ -50282,7 +50285,7 @@ "id": "publicationXrefb05", "source": "J Biol Chem", "standardName": "An interaction between a MYC protein and an EREBP protein is involved in transcriptional regulation of the rice Wx gene.", - "textContent": "10", + "textContent": "9", "type": [ "PublicationXref", "PubMed:12947109" @@ -50326,7 +50329,7 @@ "id": "publicationXrefb09", "source": "Theor Appl Genet", "standardName": "Comparison of the starch synthesis genes between maize and rice: copies, chromosome location and expression divergence.", - "textContent": "62", + "textContent": "55", "type": [ "PublicationXref", "PubMed:19593540" @@ -50365,7 +50368,7 @@ "id": "publicationXrefb19", "source": "Plant Cell", "standardName": "A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality.", - "textContent": "72", + "textContent": "69", "type": [ "PublicationXref", "PubMed:20889913" @@ -50390,7 +50393,7 @@ "id": "publicationXrefb22", "source": "Plant Cell", "standardName": "RAR1 and HSP90 form a complex with Rac/Rop GTPase and function in innate-immune responses in rice.", - "textContent": "32", + "textContent": "34", "type": [ "PublicationXref", "PubMed:18156216" @@ -50410,7 +50413,7 @@ "id": "publicationXrefb6d", "source": "Plant Mol Biol", "standardName": "OsEIL1, a rice homolog of the Arabidopsis EIN3 regulates the ethylene response as a positive component.", - "textContent": "25", + "textContent": "23", "type": [ "PublicationXref", "PubMed:16786297" @@ -50435,7 +50438,7 @@ "id": "publicationXrefb70", "source": "Mol Plant Microbe Interact", "standardName": "OsRAR1 and OsSGT1 physically interact and function in rice basal disease resistance.", - "textContent": "48", + "textContent": "51", "type": [ "PublicationXref", "PubMed:18257679" @@ -50476,7 +50479,7 @@ "id": "publicationXrefba3", "source": "FEBS J", "standardName": "Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice.", - "textContent": "55", + "textContent": "62", "type": [ "PublicationXref", "PubMed:19490115" @@ -50501,7 +50504,7 @@ "id": "publicationXrefba7", "source": "Transgenic Res", "standardName": "Analysis of the Wsi18, a stress-inducible promoter that is active in the whole grain of transgenic rice.", - "textContent": "80", + "textContent": "79", "type": [ "PublicationXref", "PubMed:20490919" @@ -50530,7 +50533,7 @@ "id": "publicationXrefbbd", "source": "Nat Genet", "standardName": "Control of rice grain-filling and yield by a gene with a potential signature of domestication.", - "textContent": "45", + "textContent": "47", "type": [ "PublicationXref", "PubMed:18820698" @@ -50556,7 +50559,7 @@ "id": "publicationXrefbc8", "source": "Plant Cell", "standardName": "RACK1 functions in rice innate immunity by interacting with the Rac1 immune complex.", - "textContent": "43", + "textContent": "45", "type": [ "PublicationXref", "PubMed:18723578" @@ -50576,7 +50579,7 @@ "id": "publicationXrefbf5", "source": "J Exp Bot", "standardName": "The syncytium-specific expression of the Orysa;KRP3 CDK inhibitor: implication of its involvement in the cell cycle control in the rice (Oryza sativa L.) syncytial endosperm.", - "textContent": "71", + "textContent": "76", "type": [ "PublicationXref", "PubMed:19933315" @@ -50601,7 +50604,7 @@ "id": "publicationXrefbfc", "source": "Plant Physiol", "standardName": "Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions.", - "textContent": "73", + "textContent": "78", "type": [ "PublicationXref", "PubMed:20335401" @@ -50621,7 +50624,7 @@ "id": "publicationXrefc02", "source": "BMB Rep", "standardName": "Identification and characterization of a rice MCM2 homologue required for DNA replication.", - "textContent": "51", + "textContent": "42", "type": [ "PublicationXref", "PubMed:18755073" @@ -50641,7 +50644,7 @@ "id": "publicationXrefc10", "source": "Plant Physiol", "standardName": "Synergism between RPBF Dof and RISBZ1 bZIP activators in the regulation of rice seed expression genes.", - "textContent": "28", + "textContent": "26", "type": [ "PublicationXref", "PubMed:16798940" @@ -50666,7 +50669,7 @@ "id": "publicationXrefc16", "source": "Plant J", "standardName": "Contribution of salicylic acid glucosyltransferase, OsSGT1, to chemically induced disease resistance in rice plants.", - "textContent": "57", + "textContent": "53", "type": [ "PublicationXref", "PubMed:18826428" @@ -50692,7 +50695,7 @@ "id": "publicationXrefc17", "source": "Plant J", "standardName": "Functional analysis of a NAC-type transcription factor OsNAC6 involved in abiotic and biotic stress-responsive gene expression in rice.", - "textContent": "31", + "textContent": "36", "type": [ "PublicationXref", "PubMed:17587305" @@ -50722,7 +50725,7 @@ "id": "publicationXrefc4c", "source": "Cell Res", "standardName": "Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight.", - "textContent": "47", + "textContent": "43", "type": [ "PublicationXref", "PubMed:19015668" @@ -50746,7 +50749,7 @@ "id": "publicationXrefc5c", "source": "Plant Physiol", "standardName": "Spatiotemporal profiling of starch biosynthesis and degradation in the developing barley grain.", - "textContent": "54", + "textContent": "58", "type": [ "PublicationXref", "PubMed:19321714" @@ -50817,7 +50820,7 @@ "id": "publicationXrefc8e", "source": "Plant Cell Physiol", "standardName": "A rice antisense SPK transformant that lacks the accumulation of seed storage substances shows no correlation between sucrose concentration in phloem sap and demand for carbon sources in the sink organs.", - "textContent": "12", + "textContent": "13", "type": [ "PublicationXref", "PubMed:15356337" @@ -50839,7 +50842,7 @@ "id": "publicationXrefcc3", "source": "Plant J", "standardName": "Interactions of two abscisic-acid induced WRKY genes in repressing gibberellin signaling in aleurone cells.", - "textContent": "24", + "textContent": "27", "type": [ "PublicationXref", "PubMed:16623886" @@ -50859,7 +50862,7 @@ "id": "publicationXrefccd", "source": "Gene", "standardName": "Characterization of a lipoate-protein ligase A gene of rice (Oryza sativa L.).", - "textContent": "40", + "textContent": "37", "type": [ "PublicationXref", "PubMed:17376611" @@ -50878,7 +50881,7 @@ "id": "publicationXrefd0b", "source": "Mol Biol Evol", "standardName": "Molecular evolution of the endosperm starch synthesis pathway genes in rice (Oryza sativa L.) and its wild ancestor, O. rufipogon L.", - "textContent": "79", + "textContent": "80", "type": [ "PublicationXref", "PubMed:20829346" @@ -50906,7 +50909,7 @@ "id": "publicationXrefd29", "source": "Cell Host Microbe", "standardName": "Activation of a Rac GTPase by the NLR family disease resistance protein Pit plays a critical role in rice innate immunity.", - "textContent": "74", + "textContent": "73", "type": [ "PublicationXref", "PubMed:20478538" @@ -50925,7 +50928,7 @@ "id": "publicationXrefd54", "source": "Plant Mol Biol", "standardName": "Characterization of OsIAA1 gene, a member of rice Aux/IAA family involved in auxin and brassinosteroid hormone responses and plant morphogenesis.", - "textContent": "56", + "textContent": "57", "type": [ "PublicationXref", "PubMed:19266169" @@ -50944,7 +50947,7 @@ "id": "publicationXrefd99", "source": "Plant Physiol", "standardName": "Rice aldehyde dehydrogenase7 is needed for seed maturation and viability.", - "textContent": "60", + "textContent": "54", "type": [ "PublicationXref", "PubMed:19052152" @@ -50973,7 +50976,7 @@ "id": "publicationXrefdbe", "source": "BMC Plant Biol", "standardName": "RNAi-directed downregulation of OsBADH2 results in aroma (2-acetyl-1-pyrroline) production in rice (Oryza sativa L.).", - "textContent": "52", + "textContent": "44", "type": [ "PublicationXref", "PubMed:18840300" @@ -50997,7 +51000,7 @@ "id": "publicationXrefdcd", "source": "Proc Natl Acad Sci U S A", "standardName": "Linking differential domain functions of the GS3 protein to natural variation of grain size in rice.", - "textContent": "75", + "textContent": "66", "type": [ "PublicationXref", "PubMed:20974950" @@ -51022,7 +51025,7 @@ "id": "publicationXrefde1", "source": "Plant Cell", "standardName": "Badh2, encoding betaine aldehyde dehydrogenase, inhibits the biosynthesis of 2-acetyl-1-pyrroline, a major component in rice fragrance.", - "textContent": "44", + "textContent": "52", "type": [ "PublicationXref", "PubMed:18599581" @@ -51064,7 +51067,7 @@ "id": "publicationXrefde9", "source": "J Exp Bot", "standardName": "Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice.", - "textContent": "76", + "textContent": "70", "type": [ "PublicationXref", "PubMed:20460361" @@ -51093,7 +51096,7 @@ "id": "publicationXrefdfc", "source": "Plant Physiol", "standardName": "Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis.", - "textContent": "23", + "textContent": "25", "type": [ "PublicationXref", "PubMed:16896230" @@ -51120,7 +51123,7 @@ "id": "publicationXrefe17", "source": "Proc Natl Acad Sci U S A", "standardName": "Molecular cloning of Sdr4, a regulator involved in seed dormancy and domestication of rice.", - "textContent": "69", + "textContent": "72", "type": [ "PublicationXref", "PubMed:20220098" @@ -51138,7 +51141,7 @@ "id": "publicationXrefe18", "source": "Plant Physiol", "standardName": "Coexpression analysis identifies Rice Starch Regulator1, a rice AP2/EREBP family transcription factor, as a novel rice starch biosynthesis regulator.", - "textContent": "66", + "textContent": "74", "type": [ "PublicationXref", "PubMed:20713616" @@ -51186,7 +51189,7 @@ "id": "publicationXrefe3b", "source": "Proc Natl Acad Sci U S A", "standardName": "A network of rice genes associated with stress response and seed development.", - "textContent": "9", + "textContent": "11", "type": [ "PublicationXref", "PubMed:12684538" @@ -51207,7 +51210,7 @@ "id": "publicationXrefe43", "source": "Biochem Biophys Res Commun", "standardName": "Characterization of alternative splicing products of bZIP transcription factors OsABI5.", - "textContent": "35", + "textContent": "33", "type": [ "PublicationXref", "PubMed:17604002" @@ -51230,7 +51233,7 @@ "id": "publicationXrefe60", "source": "Proc Natl Acad Sci U S A", "standardName": "The transcription factor IDEF1 regulates the response to and tolerance of iron deficiency in plants.", - "textContent": "34", + "textContent": "32", "type": [ "PublicationXref", "PubMed:18025467" @@ -51257,7 +51260,7 @@ "id": "publicationXrefe75", "source": "BMC Evol Biol", "standardName": "Duplication and independent selection of cell-wall invertase genes GIF1 and OsCIN1 during rice evolution and domestication.", - "textContent": "70", + "textContent": "71", "type": [ "PublicationXref", "PubMed:20416079" @@ -51309,7 +51312,7 @@ "id": "publicationXrefe7c", "source": "J Exp Bot", "standardName": "OsMTN encodes a 5'-methylthioadenosine nucleosidase that is up-regulated during submergence-induced ethylene synthesis in rice (Oryza sativa L.).", - "textContent": "30", + "textContent": "29", "type": [ "PublicationXref", "PubMed:17339651" @@ -51355,7 +51358,7 @@ "id": "publicationXrefe8d", "source": "Plant Cell Rep", "standardName": "Molecular cloning and expression analysis of the cell-wall invertase gene family in rice (Oryza sativa L.).", - "textContent": "17", + "textContent": "22", "type": [ "PublicationXref", "PubMed:15759120" @@ -51378,7 +51381,7 @@ "id": "publicationXrefe8f", "source": "Plant J", "standardName": "The rice transcription factor IDEF1 is essential for the early response to iron deficiency, and induces vegetative expression of late embryogenesis abundant genes.", - "textContent": "61", + "textContent": "59", "type": [ "PublicationXref", "PubMed:19737364" @@ -51400,7 +51403,7 @@ "id": "publicationXrefea9", "source": "Plant Mol Biol", "standardName": "Du1, encoding a novel Prp1 protein, regulates starch biosynthesis through affecting the splicing of Wxb pre-mRNAs in rice (Oryza sativa L.).", - "textContent": "33", + "textContent": "35", "type": [ "PublicationXref", "PubMed:17579813" @@ -51451,7 +51454,7 @@ "id": "publicationXrefebe", "source": "Mol Genet Genomics", "standardName": "The abiotic stress-responsive NAC-type transcription factor OsNAC5 regulates stress-inducible genes and stress tolerance in rice.", - "textContent": "67", + "textContent": "75", "type": [ "PublicationXref", "PubMed:20632034" @@ -51471,7 +51474,7 @@ "id": "publicationXrefece", "source": "Theor Appl Genet", "standardName": "Over-expression of a LEA gene in rice improves drought resistance under the field conditions.", - "textContent": "37", + "textContent": "30", "type": [ "PublicationXref", "PubMed:17426956" @@ -51492,7 +51495,7 @@ "id": "publicationXrefed7", "source": "Plant Physiol", "standardName": "Down-regulation of metallothionein, a reactive oxygen scavenger, by the small GTPase OsRac1 in rice.", - "textContent": "13", + "textContent": "12", "type": [ "PublicationXref", "PubMed:15220467" @@ -51529,7 +51532,7 @@ "id": "publicationXrefedb", "source": "Plant J", "standardName": "Inactivation of the CTD phosphatase-like gene OsCPL1 enhances the development of the abscission layer and seed shattering in rice.", - "textContent": "78", + "textContent": "67", "type": [ "PublicationXref", "PubMed:19807881" @@ -51547,7 +51550,7 @@ "id": "publicationXrefeee", "source": "Planta", "standardName": "Structural and enzymatic characterization of the isoamylase1 homo-oligomer and the isoamylase1-isoamylase2 hetero-oligomer from rice endosperm.", - "textContent": "26", + "textContent": "24", "type": [ "PublicationXref", "PubMed:16953433" @@ -51569,7 +51572,7 @@ "id": "publicationXrefefc", "source": "Planta", "standardName": "Identification of three shikimate kinase genes in rice: characterization of their differential expression during panicle development and of the enzymatic activities of the encoded proteins.", - "textContent": "22", + "textContent": "21", "type": [ "PublicationXref", "PubMed:15891897" @@ -51592,7 +51595,7 @@ "id": "publicationXreff15", "source": "J Exp Bot", "standardName": "Expression profiling of genes involved in starch synthesis in sink and source organs of rice.", - "textContent": "21", + "textContent": "19", "type": [ "PublicationXref", "PubMed:16275672" @@ -51615,7 +51618,7 @@ "id": "publicationXreff34", "source": "Planta", "standardName": "Interaction between proliferating cell nuclear antigen and JUN-activation-domain-binding protein 1 in the meristem of rice, Oryza sativa L.", - "textContent": "11", + "textContent": "10", "type": [ "PublicationXref", "PubMed:12783325" @@ -51641,7 +51644,7 @@ "id": "publicationXreff43", "source": "Plant Cell Rep", "standardName": "Knockout of a starch synthase gene OsSSIIIa/Flo5 causes white-core floury endosperm in rice (Oryza sativa L.).", - "textContent": "29", + "textContent": "31", "type": [ "PublicationXref", "PubMed:17297616" @@ -51664,7 +51667,7 @@ "id": "publicationXreff4a", "source": "Plant Cell Physiol", "standardName": "Characterization of the reactions of starch branching enzymes from rice endosperm.", - "textContent": "65", + "textContent": "68", "type": [ "PublicationXref", "PubMed:20305271" @@ -51725,7 +51728,7 @@ "id": "publicationXreff8b", "source": "Planta", "standardName": "The cell cycle genes cycA1;1 and cdc2Os-3 are coordinately regulated by gibberellin in planta.", - "textContent": "6", + "textContent": "7", "type": [ "PublicationXref", "PubMed:10987556" @@ -51748,7 +51751,7 @@ "id": "publicationXreff97", "source": "Plant Cell Physiol", "standardName": "Hormonal cross-talk between auxin and ethylene differentially regulates the expression of two members of the 1-aminocyclopropane-1-carboxylate oxidase gene family in rice (Oryza sativa L.).", - "textContent": "7", + "textContent": "6", "type": [ "PublicationXref", "PubMed:10805599" @@ -51777,7 +51780,7 @@ "id": "publicationXreffb5", "source": "Plant Cell Environ", "standardName": "Increased nitrogen-use efficiency in transgenic rice plants over-expressing a nitrogen-responsive early nodulin gene identified from rice expression profiling.", - "textContent": "59", + "textContent": "56", "type": [ "PublicationXref", "PubMed:19682292" @@ -51797,7 +51800,7 @@ "id": "publicationXreffc4", "source": "Plant Physiol", "standardName": "Comprehensive expression profiling of rice grain filling-related genes under high temperature using DNA microarray.", - "textContent": "36", + "textContent": "40", "type": [ "PublicationXref", "PubMed:17384160" @@ -51836,7 +51839,7 @@ "id": "publicationXreffd4", "source": "Plant Physiol", "standardName": "A rice WRKY gene encodes a transcriptional repressor of the gibberellin signaling pathway in aleurone cells.", - "textContent": "16", + "textContent": "14", "type": [ "PublicationXref", "PubMed:15047897" @@ -51863,7 +51866,7 @@ "id": "publicationXreffd6", "source": "Genetics", "standardName": "Evolutionary history of GS3, a gene conferring grain length in rice.", - "textContent": "53", + "textContent": "63", "type": [ "PublicationXref", "PubMed:19506305" @@ -51881,7 +51884,7 @@ "id": "publicationXrefff5", "source": "Planta", "standardName": "A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.).", - "textContent": "15", + "textContent": "16", "type": [ "PublicationXref", "PubMed:15232694" @@ -51903,7 +51906,7 @@ "id": "publicationXrefff9", "source": "Plant Physiol", "standardName": "Overexpression of the transcription factor AP37 in rice improves grain yield under drought conditions.", - "textContent": "58", + "textContent": "60", "type": [ "PublicationXref", "PubMed:19429605" @@ -51917,10 +51920,10 @@ "@context": [ "https://cdn.rawgit.com/wikipathways/WpVocabularies/7a46a05/contexts/pvjs.jsonld", { - "@base": "http://identifiers.org/wikipathways/WP2199/" + "@base": "WP2199/" } ], - "author": "[Mamatha, Pjaiswal, MaintBot, L Dupuis, Eweitz, Larsgw]", + "author": "[Mamatha, Pjaiswal, MaintBot, L Dupuis, Eweitz, Larsgw, Egonw]", "comments": [ { "content": "The network features protein-protein interactions related to seed development in rice. Co-expression information for some genes known to be important for seed development is also shown. \r\nThe Gene Basket contains a few genes/proteins that are known to be important for the process but for which interactions were unknown or intentionally left out when the network was created.\r\nPlease go ahead and move them into the network if you find the correct interacting partner(s).", @@ -52816,7 +52819,7 @@ "bca44", "af8ee" ], - "dataSourceVersion": "WP2199_r125282", + "dataSourceVersion": "WP2199_r134214", "displayName": "Seed development", "drawAs": "rect", "fill": "white", @@ -52824,9 +52827,9 @@ "fontWeight": "bold", "gpmlElementName": "Pathway", "height": 3788.999999999997, - "id": "http://identifiers.org/wikipathways/WP2199", + "id": "WP2199", "kaavioType": "Group", - "lastModified": "20230131161914", + "lastModified": "20240717074828", "name": "Seed development", "organism": "Oryza sativa", "padding": 5, @@ -52835,7 +52838,7 @@ "stroke": "black", "strokeWidth": 0, "textAlign": "left", - "textContent": "Name: Seed development\nLast Modified: 20230131161914\nOrganism: Oryza sativa", + "textContent": "Name: Seed development\nLast Modified: 20240717074828\nOrganism: Oryza sativa", "type": [ "Pathway", "http://identifiers.org/pw/PW:0000003" diff --git a/pathways/WP2199/WP2199.png b/pathways/WP2199/WP2199.png index bc5dec725..fb53d333f 100644 Binary files a/pathways/WP2199/WP2199.png and b/pathways/WP2199/WP2199.png differ diff --git a/pathways/WP2199/WP2199.svg b/pathways/WP2199/WP2199.svg index 4e4b95af4..220c5091c 100644 --- a/pathways/WP2199/WP2199.svg +++ b/pathways/WP2199/WP2199.svg @@ -1,5 +1,5 @@ - + @@ -574,8 +574,8 @@ - - + + @@ -5846,9 +5846,9 @@ Seed Development - + Name: Seed development - Last Modified: 20230131161914 + Last Modified: 20240717074828 Organism: Oryza sativa diff --git a/pathways/WP2233/WP2233-bibliography.tsv b/pathways/WP2233/WP2233-bibliography.tsv index 2beb4db93..2790d2a0d 100644 --- a/pathways/WP2233/WP2233-bibliography.tsv +++ b/pathways/WP2233/WP2233-bibliography.tsv @@ -1,5 +1,5 @@ ID Database Citation -18050470 Pubmed "Ewbank JJ. Signaling in the immune response. WormBook. 2006 Jan 23;1–12. PubMed Europe PMC Scholia" -19198592 Pubmed "Zugasti O, Ewbank JJ. Neuroimmune regulation of antimicrobial peptide expression by a noncanonical TGF-beta signaling pathway in Caenorhabditis elegans epidermis. Nat Immunol. 2009 Mar;10(3):249–56. PubMed Europe PMC Scholia" -21575913 Pubmed "Dierking K, Polanowska J, Omi S, Engelmann I, Gut M, Lembo F, et al. Unusual regulation of a STAT protein by an SLC6 family transporter in C. elegans epidermal innate immunity. Cell Host Microbe. 2011 May 19;9(5):425–35. PubMed Europe PMC Scholia" -25086774 Pubmed "Zugasti O, Bose N, Squiban B, Belougne J, Kurz CL, Schroeder FC, et al. Activation of a G protein-coupled receptor by its endogenous ligand triggers the innate immune response of Caenorhabditis elegans. Nat Immunol. 2014 Sep;15(9):833–8. PubMed Europe PMC Scholia" +18050470 Pubmed "Signaling in the immune response. Ewbank JJ. WormBook. 2006 Jan 23;1–12. PubMed Europe PMC Scholia" +19198592 Pubmed "Neuroimmune regulation of antimicrobial peptide expression by a noncanonical TGF-beta signaling pathway in Caenorhabditis elegans epidermis. Zugasti O, Ewbank JJ. Nat Immunol. 2009 Mar;10(3):249–56. PubMed Europe PMC Scholia" +21575913 Pubmed "Unusual regulation of a STAT protein by an SLC6 family transporter in C. elegans epidermal innate immunity. Dierking K, Polanowska J, Omi S, Engelmann I, Gut M, Lembo F, et al. Cell Host Microbe. 2011 May 19;9(5):425–35. PubMed Europe PMC Scholia" +25086774 Pubmed "Activation of a G protein-coupled receptor by its endogenous ligand triggers the innate immune response of Caenorhabditis elegans. Zugasti O, Bose N, Squiban B, Belougne J, Kurz CL, Schroeder FC, et al. Nat Immunol. 2014 Sep;15(9):833–8. PubMed Europe PMC Scholia" diff --git a/pathways/WP2233/WP2233-datanodes.tsv b/pathways/WP2233/WP2233-datanodes.tsv index 9704e1147..58dc06221 100644 --- a/pathways/WP2233/WP2233-datanodes.tsv +++ b/pathways/WP2233/WP2233-datanodes.tsv @@ -1,29 +1,24 @@ -Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI -PIP2 Metabolite chebi:18348 wikidata:Q28797894 chebi:18348;chebi:18348 -IP3 Metabolite chebi:16595 wikidata:Q26998374 chebi:16595;chebi:16595 inchikey:MMWCIQZXVOZEGG-XJTPDSDZSA-N -DAG Metabolite chebi:18035 diacylglycerol wikidata:Q161466 chebi:18035;chebi:18035 -HPLA Metabolite hmdb:HMDB0000755 Through targeted metabolomics analysis we identified the tyrosine derivative 4-hydroxyphenyllactic acid (HPLA) as an endogenous ligand. Our findings reveal DCAR-1 and its cognate ligand HPLA to be triggers of the epidermal innate immune response in C. elegans and highlight the ancient role of GPCRs in host defense.
Type your comment here chebi:17385;chebi:17385 inchikey:JVGVDSSUAVXRDY-UHFFFAOYSA-N -DBL-1 GeneProduct wormbase:T25F10.2 -NIPI-4 GeneProduct wormbase:F40A3.5 NIPI-4 phenocopies STA-2 and SNF-12 -ELT-3 GeneProduct wormbase:K02B9.4 -DCAR-1 GeneProduct wormbase:C06H5.7 -SMA-3 GeneProduct wormbase:R13F6.9 Neither SMA-2 nor SMA-4 are required in this DBL-1 triggered response
Type your comment here -cnc-2 GeneProduct wormbase:R09B5.3 -nlp-29 GeneProduct wormbase:B0213.4 -PMK-1 GeneProduct wormbase:B0218.3 -SEK-1 GeneProduct wormbase:R03G5.2 -NSY-1 GeneProduct wormbase:F59A6.1 -PKC-3 GeneProduct wormbase:F09E5.1 -TIR-1B GeneProduct wormbase:F13B10.1 -TPA-1(PKC delta) GeneProduct wormbase:B0545.1 -PLC-3 GeneProduct wormbase:T01E8.3 -GPA-12(Galpha) GeneProduct wormbase:F18G5.3 -NIPI-3 GeneProduct wormbase:K09A9.1 -RACK-1(Gbeta) GeneProduct wormbase:K04D7.1 -EGL-8 (PLCbeta) GeneProduct wormbase:B0348.4 -STA-2 GeneProduct wormbase:F58E6.1 -STA-2 GeneProduct wormbase:F58E6.1 -STA-2 GeneProduct wormbase:F58E6.1 -STA-2 GeneProduct wormbase:F58E6.1 -STA-2 GeneProduct wormbase:F58E6.1 -NIPI-4 GeneProduct wormbase:F40A3.5 NIPI-4 phenocopies STA-2 and SNF-12 +Label Type Identifier Comment Ensembl NCBI gene HGNC UniProt Wikidata ChEBI InChI PubChem ChemSpider HMDB KEGG LipidMaps +PIP2 Metabolite chebi:18348 "" wikidata:Q28797894 chebi:18348 kegg.compound:C04637 +IP3 Metabolite chebi:16595 "" wikidata:Q26998374 chebi:16595 inchikey:MMWCIQZXVOZEGG-XJTPDSDZSA-N pubchem.compound:439456 chemspider:388562 hmdb:HMDB0001498 kegg.compound:C01245 +DAG Metabolite chebi:18035 "diacylglycerol" wikidata:Q161466 chebi:18035 kegg.compound:C00165 lipidmaps:LMGL0201 +HPLA Metabolite hmdb:HMDB0000755 "Through targeted metabolomics analysis we identified the tyrosine derivative 4-hydroxyphenyllactic acid (HPLA) as an endogenous ligand. Our findings reveal DCAR-1 and its cognate ligand HPLA to be triggers of the epidermal innate immune response in C. elegans and highlight the ancient role of GPCRs in host defense." chebi:17385 inchikey:JVGVDSSUAVXRDY-UHFFFAOYSA-N pubchem.compound:9378 chemspider:9010 hmdb:HMDB0000755 kegg.compound:C03672 +DBL-1 GeneProduct wormbase:T25F10.2 "" +NIPI-4 GeneProduct wormbase:F40A3.5 "NIPI-4 phenocopies STA-2 and SNF-12" +ELT-3 GeneProduct wormbase:K02B9.4 "" +DCAR-1 GeneProduct wormbase:C06H5.7 "" +SMA-3 GeneProduct wormbase:R13F6.9 "Neither SMA-2 nor SMA-4 are required in this DBL-1 triggered response" +cnc-2 GeneProduct wormbase:R09B5.3 "" +nlp-29 GeneProduct wormbase:B0213.4 "" +PMK-1 GeneProduct wormbase:B0218.3 "" +SEK-1 GeneProduct wormbase:R03G5.2 "" +NSY-1 GeneProduct wormbase:F59A6.1 "" +PKC-3 GeneProduct wormbase:F09E5.1 "" +TIR-1B GeneProduct wormbase:F13B10.1 "" +TPA-1(PKC delta) GeneProduct wormbase:B0545.1 "" +PLC-3 GeneProduct wormbase:T01E8.3 "" +GPA-12(Galpha) GeneProduct wormbase:F18G5.3 "" +NIPI-3 GeneProduct wormbase:K09A9.1 "" +RACK-1(Gbeta) GeneProduct wormbase:K04D7.1 "" +EGL-8 (PLCbeta) GeneProduct wormbase:B0348.4 "" +STA-2 GeneProduct wormbase:F58E6.1 "" diff --git a/pathways/WP2233/WP2233.gpml b/pathways/WP2233/WP2233.gpml index cc142649f..4144986a7 100644 --- a/pathways/WP2233/WP2233.gpml +++ b/pathways/WP2233/WP2233.gpml @@ -1,5 +1,5 @@ - + "Regulation of immune responses in the epidermis by two largely parallel pathways. The p38 MAPK pathway (proteins in this pathway are in black letters) regulates the expression nlp-29, an AMP-encoding gene. A second AMP, encoded by cnc-2, is regulated by neuronally expressed dbl-1 that actives TGFb pathway (blue letters) in the epidermis. The identity of the neurones and whether G-protein signalling is required for neuronal secretion of DBL-1 is not known." ff4 @@ -37,7 +37,6 @@ actives TGFb pathway (blue letters) in the epidermis. The identity of the neuron Through targeted metabolomics analysis we identified the tyrosine derivative 4-hydroxyphenyllactic acid (HPLA) as an endogenous ligand. Our findings reveal DCAR-1 and its cognate ligand HPLA to be triggers of the epidermal innate immune response in C. elegans and highlight the ancient role of GPCRs in host defense. - Type your comment here e95 @@ -65,7 +64,6 @@ actives TGFb pathway (blue letters) in the epidermis. The identity of the neuron Neither SMA-2 nor SMA-4 are required in this DBL-1 triggered response - Type your comment here d29 @@ -155,50 +153,50 @@ actives TGFb pathway (blue letters) in the epidermis. The identity of the neuron Results indicate that sma-6 acts in the epidermis to regulate cnc-2 expression and suggest that SMA-6 and DAF-4 act in the cell-autonomous way to transduce a DBL-1 signal associated with fungal infection. d29 - - + + - - + + - - + + - - + + - - + + - - + + - - + + @@ -206,129 +204,128 @@ actives TGFb pathway (blue letters) in the epidermis. The identity of the neuron SNF-12 physically interacts with STA-2, possibly tethering STA-2 in the cytosol. STA-2 and SNF-12 function together to regulate AMP gene expression. be7 - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + Epistatic relationship between SMA-3 and SNF-12 is unknown - Type your comment here - - + + - - + + @@ -366,11 +363,21 @@ actives TGFb pathway (blue letters) in the epidermis. The identity of the neuron - - signaling pathway in the innate immune response - PW:0000819 - Pathway Ontology - + + 21575913 + PubMed + Unusual regulation of a STAT protein by an SLC6 family transporter in C. elegans epidermal innate immunity. + Cell Host Microbe + 2011 + Dierking K + Polanowska J + Omi S + Engelmann I + Gut M + Lembo F + Ewbank JJ + Pujol N + 18050470 PubMed @@ -379,15 +386,6 @@ actives TGFb pathway (blue letters) in the epidermis. The identity of the neuron 2006 Ewbank JJ - - 19198592 - PubMed - Neuroimmune regulation of antimicrobial peptide expression by a noncanonical TGF-beta signaling pathway in Caenorhabditis elegans epidermis. - Nat Immunol - 2009 - Zugasti O - Ewbank JJ - 25086774 PubMed @@ -403,20 +401,20 @@ actives TGFb pathway (blue letters) in the epidermis. The identity of the neuron Pujol N Ewbank JJ - - 21575913 + + 19198592 PubMed - Unusual regulation of a STAT protein by an SLC6 family transporter in C. elegans epidermal innate immunity. - Cell Host Microbe - 2011 - Dierking K - Polanowska J - Omi S - Engelmann I - Gut M - Lembo F + Neuroimmune regulation of antimicrobial peptide expression by a noncanonical TGF-beta signaling pathway in Caenorhabditis elegans epidermis. + Nat Immunol + 2009 + Zugasti O Ewbank JJ - Pujol N + + signaling pathway in the innate immune response + PW:0000819 + Pathway Ontology + + diff --git a/pathways/WP2233/WP2233.json b/pathways/WP2233/WP2233.json index ca7185b06..0af6f5116 100644 --- a/pathways/WP2233/WP2233.json +++ b/pathways/WP2233/WP2233.json @@ -61,7 +61,6 @@ 0.5 ] }, - "id": "c0e9d", "isAttachedTo": "a8384", "orientation": [ 1, @@ -81,7 +80,6 @@ 0 ] }, - "id": "ef03b", "isAttachedTo": "b5109", "orientation": [ 0, @@ -192,7 +190,6 @@ 1 ] }, - "id": "a53b6", "isAttachedTo": "cf244", "orientation": [ 0, @@ -212,7 +209,6 @@ 0 ] }, - "id": "dff98", "isAttachedTo": "dd3e2", "orientation": [ 0, @@ -263,7 +259,7 @@ "PIP2", "Wikidata:Q28797894", "ChEBI:18348", - "ChEBI:18348" + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -413,7 +409,6 @@ 1 ] }, - "id": "edba4", "isAttachedTo": "f5be0", "orientation": [ 0, @@ -433,7 +428,6 @@ 0 ] }, - "id": "c1bd2", "isAttachedTo": "f3859", "orientation": [ 0, @@ -558,8 +552,11 @@ "IP3", "Wikidata:Q26998374", "ChEBI:16595", - "ChEBI:16595", - "InChI:MMWCIQZXVOZEGG-XJTPDSDZSA-N" + "InChI:MMWCIQZXVOZEGG-XJTPDSDZSA-N", + "", + "", + "", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -605,7 +602,8 @@ "DAG", "Wikidata:Q161466", "ChEBI:18035", - "ChEBI:18035" + "", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -1143,9 +1141,6 @@ "comments": [ { "content": "Through targeted metabolomics analysis we identified the tyrosine derivative 4-hydroxyphenyllactic acid (HPLA) as an endogenous ligand. Our findings reveal DCAR-1 and its cognate ligand HPLA to be triggers of the epidermal innate immune response in C. elegans and highlight the ancient role of GPCRs in host defense." - }, - { - "content": "Type your comment here" } ], "drawAs": "none", @@ -1175,8 +1170,11 @@ "CompactIdentifier:hmdb:HMDB0000755", "HPLA", "ChEBI:17385", - "ChEBI:17385", - "InChI:JVGVDSSUAVXRDY-UHFFFAOYSA-N" + "InChI:JVGVDSSUAVXRDY-UHFFFAOYSA-N", + "", + "", + "", + "" ], "verticalAlign": "middle", "whiteSpace": "pre", @@ -1257,7 +1255,6 @@ 0.5 ] }, - "id": "ba416", "isAttachedTo": "af186", "orientation": [ 1, @@ -1277,7 +1274,6 @@ 0.5 ] }, - "id": "bd07d", "isAttachedTo": "b3bd4", "orientation": [ 1, @@ -1530,9 +1526,6 @@ "comments": [ { "content": "Epistatic relationship between SMA-3 and SNF-12 is unknown" - }, - { - "content": "Type your comment here" } ], "drawAs": "StraightLine", @@ -1557,7 +1550,6 @@ 1 ] }, - "id": "d91ae", "isAttachedTo": "fdfc9", "orientation": [ 0, @@ -1577,7 +1569,6 @@ 0 ] }, - "id": "a2f2b", "isAttachedTo": "c0bca", "orientation": [ 0, @@ -1827,12 +1818,10 @@ "markerEnd": "MimTranscriptionTranslation", "points": [ { - "id": "f078e", "x": 312.8607888631091, "y": 686.93271461717 }, { - "id": "c7687", "x": 383.626450116009, "y": 686.9327146171696 } @@ -1956,9 +1945,6 @@ "comments": [ { "content": "Neither SMA-2 nor SMA-4 are required in this DBL-1 triggered response" - }, - { - "content": "Type your comment here" } ], "drawAs": "rect", @@ -2031,7 +2017,6 @@ 1 ] }, - "id": "f2def", "isAttachedTo": "f3859", "orientation": [ 0, @@ -2051,7 +2036,6 @@ 0 ] }, - "id": "d4280", "isAttachedTo": "bc7f0", "orientation": [ 0, @@ -2077,12 +2061,10 @@ "kaavioType": "Edge", "points": [ { - "id": "da81a", "x": 317, "y": 686 }, { - "id": "bfc0d", "x": 481, "y": 686 } @@ -2104,12 +2086,10 @@ "markerEnd": "MimTranscriptionTranslation", "points": [ { - "id": "d41ef", "x": 261.8607888631091, "y": 739.93271461717 }, { - "id": "fbd61", "x": 332.626450116009, "y": 739.9327146171696 } @@ -2130,12 +2110,10 @@ "kaavioType": "Edge", "points": [ { - 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"id": "bf3f2", "x": 338.01020408163265, "y": 647.9591836734694 } @@ -2783,7 +2741,6 @@ 1 ] }, - "id": "e1a2d", "isAttachedTo": "c836d", "orientation": [ 0, @@ -2803,7 +2760,6 @@ 0 ] }, - "id": "f62b8", "isAttachedTo": "dbd7c", "orientation": [ 0, @@ -2845,7 +2801,6 @@ 1 ] }, - "id": "be5fc", "isAttachedTo": "bef80", "orientation": [ 0, @@ -2865,7 +2820,6 @@ 0 ] }, - "id": "de5c5", "isAttachedTo": "a60b7", "orientation": [ 0, @@ -2905,7 +2859,6 @@ 1 ] }, - "id": "ede42", "isAttachedTo": "aca02", "orientation": [ 0, @@ -2915,7 +2868,6 @@ "y": 254 }, { - "id": "a0f4e", "x": 309, "y": 288 } @@ -2955,7 +2907,6 @@ 0.5 ] }, - "id": "dbb2b", "isAttachedTo": "a8384", "orientation": [ 1, @@ -2975,7 +2926,6 @@ 0.5 ] }, - "id": "e6961", "isAttachedTo": "b6275", "orientation": [ 1, @@ -3016,7 +2966,6 @@ 1 ] }, - "id": "a07d4", "isAttachedTo": "b6275", "orientation": [ 0, @@ -3036,7 +2985,6 @@ 0 ] }, - "id": "ba839", "isAttachedTo": "b6d3e", "orientation": [ 0, @@ -3146,7 +3094,7 @@ "@context": [ "https://cdn.rawgit.com/wikipathways/WpVocabularies/7a46a05/contexts/pvjs.jsonld", { - "@base": "http://identifiers.org/wikipathways/WP2233/" + "@base": "WP2233/" } ], "author": "[Kyook, MaintBot, Susan, Egonw]", @@ -3226,7 +3174,7 @@ "a0605", "e33da" ], - "dataSourceVersion": "WP2233_r120941", + "dataSourceVersion": "WP2233_r134215", "displayName": "Immune responses in the epidermis", "drawAs": "rect", "fill": "white", @@ -3234,9 +3182,9 @@ "fontWeight": "bold", "gpmlElementName": "Pathway", "height": 835, - "id": "http://identifiers.org/wikipathways/WP2233", + "id": "WP2233", "kaavioType": "Group", - "lastModified": "20220202062325", + "lastModified": "20240717074940", "name": "Immune responses in the epidermis", "organism": "Caenorhabditis elegans", "padding": 5, @@ -3245,7 +3193,7 @@ "stroke": "black", "strokeWidth": 0, "textAlign": "left", - "textContent": "Name: Immune responses in the epidermis\nLast Modified: 20220202062325\nOrganism: Caenorhabditis elegans", + "textContent": "Name: Immune responses in the epidermis\nLast Modified: 20240717074940\nOrganism: Caenorhabditis elegans", "type": [ "Pathway", "http://identifiers.org/pw/PW:0000819" diff --git a/pathways/WP2233/WP2233.png b/pathways/WP2233/WP2233.png index ea61a6cee..86fa5bd58 100644 Binary files a/pathways/WP2233/WP2233.png and b/pathways/WP2233/WP2233.png differ diff --git a/pathways/WP2233/WP2233.svg b/pathways/WP2233/WP2233.svg index d83ca2f06..0cb25d8b6 100644 --- a/pathways/WP2233/WP2233.svg +++ b/pathways/WP2233/WP2233.svg @@ -1,5 +1,5 @@ - + @@ -460,8 +460,8 @@ - - + + @@ -523,8 +523,8 @@ - - + + @@ -837,9 +837,9 @@ NIPI-4 - + Name: Immune responses in the epidermis - Last Modified: 20220202062325 + Last Modified: 20240717074940 Organism: Caenorhabditis elegans diff --git a/pathways/WP5110/WP5110.gpml b/pathways/WP5110/WP5110.gpml index 48e9ab45b..25234926b 100644 --- a/pathways/WP5110/WP5110.gpml +++ b/pathways/WP5110/WP5110.gpml @@ -474,71 +474,62 @@ - - 31676439 + + 28882953 PubMed - Interleukin 10 promotes macrophage uptake of HDL and LDL by stimulating fluid-phase endocytosis. - Biochim Biophys Acta Mol Cell Biol Lipids - 2020 - Lucero D - Islam P - Freeman LA - Jin X - Pryor M - Tang J - Kruth HS - Remaley AT + <i>SCARB1</i>Gene Polymorphisms and HDL Subfractions in Coronary Artery Disease. + In Vivo + 2017 + Ayhan H + Gormus U + Isbir S + Yilmaz SG + Isbir T - - hyperlipoproteinemia type III - DOID:3145 - Disease - - - 32120838 + + 28098593 PubMed - Association between the<i>APOA2</i>rs3813627 Single Nucleotide Polymorphism and HDL and APOA1 Levels Through BMI. - Biomedicines - 2020 - Boughanem H - Bandera-Merchán B - Hernández-Alonso P - Moreno-Morales N - Tinahones FJ - Lozano J - Morcillo S - Macias-Gonzalez M + Familial dysbetalipoproteinemia: an underdiagnosed lipid disorder. + Curr Opin Endocrinol Diabetes Obes + 2017 + Koopal C + Marais AD + Visseren FL - - familial hyperlipidemia - DOID:1168 - Disease - - - 30420806 + + 29100061 PubMed - Sexually Dimorphic Regulation of EET Synthesis and Metabolism: Roles of Estrogen. - Front Pharmacol - 2018 - Huang A - Sun D + Apolipoprotein C-II: New findings related to genetics, biochemistry, and role in triglyceride metabolism. + Atherosclerosis + 2017 + Wolska A + Dunbar RL + Freeman LA + Ueda M + Amar MJ + Sviridov DO + Remaley AT - - 31462513 + + 30249788 PubMed - Identification of ApoA4 as a sphingosine 1-phosphate chaperone in ApoM- and albumin-deficient mice. + N-terminal mutation of apoA-I and interaction with ABCA1 reveal mechanisms of nascent HDL biogenesis. J Lipid Res 2019 - Obinata H - Kuo A - Wada Y - Swendeman S - Liu CH - Blaho VA - Nagumo R - Satoh K - Izumi T - Hla T + Liu M + Mei X + Herscovitz H + Atkinson D + + + 20301485 + PubMed + Familial Lipoprotein Lipase Deficiency + + 1993 + Burnett JR + Hooper AJ + Hegele RA 24426196 @@ -549,40 +540,6 @@ Todur SP Ashavaid TF - - 28098593 - PubMed - Familial dysbetalipoproteinemia: an underdiagnosed lipid disorder. - Curr Opin Endocrinol Diabetes Obes - 2017 - Koopal C - Marais AD - Visseren FL - - - 22461740 - PubMed - Low-density lipoprotein receptor (LDLR) family orchestrates cholesterol homeostasis. - Yale J Biol Med - 2012 - Go GW - Mani A - - - 31676439 - PubMed - Interleukin 10 promotes macrophage uptake of HDL and LDL bystimulating fluid-phase endocytosis. - Biochim Biophys Acta Mol Cell Biol Lipids - 2020 - Lucero D - Islam P - Freeman LA - Jin X - Pryor M - Tang J - Kruth HS - Remaley AT - 29057873 PubMed @@ -601,27 +558,40 @@ Kovalik JP Kim JB - - 24426196 + + 30420806 PubMed - Association of CETP and LIPC Gene Polymorphisms with HDL and LDL Sub-fraction Levels in a Group of Indian Subjects: A Cross-Sectional Study. - Indian J Clin Biochem - 2013 - Todur SP - Ashavaid TF + Sexually Dimorphic Regulation of EET Synthesis and Metabolism: Roles of Estrogen. + Front Pharmacol + 2018 + Huang A + Sun D - - 30249788 + + 31676439 PubMed - N-terminal mutation of apoA-I and interaction with ABCA1 reveal mechanisms of nascent HDL biogenesis. - J Lipid Res - 2019 - Liu M - Mei X - Herscovitz H - Atkinson D + Interleukin 10 promotes macrophage uptake of HDL and LDL by stimulating fluid-phase endocytosis. + Biochim Biophys Acta Mol Cell Biol Lipids + 2020 + Lucero D + Islam P + Freeman LA + Jin X + Pryor M + Tang J + Kruth HS + Remaley AT - + + 14592533 + PubMed + The role of scavenger receptor class B type I (SR-BI) in lipid trafficking. defining the rules for lipid traders. + Int J Biochem Cell Biol + 2004 + Rhainds D + Brissette L + + 22461740 PubMed Low-density lipoprotein receptor (LDLR) family orchestrates cholesterol homeostasis. @@ -630,37 +600,45 @@ Go GW Mani A - - 29100061 + + hyperlipoproteinemia type III + DOID:3145 + Disease + + + hepatocyte + CL:0000182 + Cell Type + + + 24426196 PubMed - Apolipoprotein C-II: New findings related to genetics, biochemistry, and role in triglyceride metabolism. - Atherosclerosis - 2017 - Wolska A - Dunbar RL - Freeman LA - Ueda M - Amar MJ - Sviridov DO - Remaley AT + Association of CETP and LIPC Gene Polymorphisms with HDL and LDL Sub-fraction Levels in a Group of Indian Subjects: A Cross-Sectional Study. + Indian J Clin Biochem + 2013 + Todur SP + Ashavaid TF - - 23055695 + + 14592533 PubMed - Cholesteryl ester transfer protein inhibitors for dyslipidemia: focus on dalcetrapib. - Drug Des Devel Ther - 2012 - Goldberg AS - Hegele RA + The role of scavenger receptor class B type I (SR-BI) in lipid trafficking. defining the rules for lipid traders. + Int J Biochem Cell Biol + 2004 + Rhainds D + Brissette L - - 28766509 + + 28882953 PubMed - High-density lipoprotein metabolism and reverse cholesterol transport: strategies for raising HDL cholesterol. - Anatol J Cardiol + <i>SCARB1</i>Gene Polymorphisms and HDL Subfractions in Coronary Artery Disease. + In Vivo 2017 - Tosheska Trajkovska K - Topuzovska S + Ayhan H + Gormus U + Isbir S + Yilmaz SG + Isbir T 30333156 @@ -676,57 +654,50 @@ Hegele RA Schaefer EJ - - hepatocyte - CL:0000182 - Cell Type - - - 30333156 + + 23055695 PubMed - Genetic and secondary causes of severe HDL deficiency and cardiovascular disease. - J Lipid Res - 2018 - Geller AS - Polisecki EY - Diffenderfer MR - Asztalos BF - Karathanasis SK + Cholesteryl ester transfer protein inhibitors for dyslipidemia: focus on dalcetrapib. + Drug Des Devel Ther + 2012 + Goldberg AS Hegele RA - Schaefer EJ - - 29100061 + + 26247089 PubMed - Apolipoprotein C-II: New findings related to genetics, biochemistry, and role in triglyceride metabolism. - Atherosclerosis - 2017 - Wolska A - Dunbar RL - Freeman LA - Ueda M - Amar MJ - Sviridov DO - Remaley AT + Introduction to Lipids and Lipoproteins + + 2000 + Feingold KR - - 14592533 + + 31462513 PubMed - The role of scavenger receptor class B type I (SR-BI) in lipid trafficking. defining the rules for lipid traders. - Int J Biochem Cell Biol - 2004 - Rhainds D - Brissette L + Identification of ApoA4 as a sphingosine 1-phosphate chaperone in ApoM- and albumin-deficient mice. + J Lipid Res + 2019 + Obinata H + Kuo A + Wada Y + Swendeman S + Liu CH + Blaho VA + Nagumo R + Satoh K + Izumi T + Hla T - - 25328986 + + 22461740 PubMed - Apolipoprotein E isoforms and lipoprotein metabolism. - IUBMB Life - 2014 - Phillips MC + Low-density lipoprotein receptor (LDLR) family orchestrates cholesterol homeostasis. + Yale J Biol Med + 2012 + Go GW + Mani A - + 30249788 PubMed N-terminal mutation of apoA-I and interaction with ABCA1 reveal mechanisms of nascent HDL biogenesis. @@ -737,19 +708,26 @@ Herscovitz H Atkinson D - - 28882953 + + 30333156 PubMed - <i>SCARB1</i>Gene Polymorphisms and HDL Subfractions in Coronary Artery Disease. - In Vivo - 2017 - Ayhan H - Gormus U - Isbir S - Yilmaz SG - Isbir T + Genetic and secondary causes of severe HDL deficiency and cardiovascular disease. + J Lipid Res + 2018 + Geller AS + Polisecki EY + Diffenderfer MR + Asztalos BF + Karathanasis SK + Hegele RA + Schaefer EJ - + + disease pathway + PW:0000013 + Pathway Ontology + + 32120838 PubMed Association between the<i>APOA2</i>rs3813627 Single Nucleotide Polymorphism and HDL and APOA1 Levels Through BMI. @@ -764,15 +742,62 @@ Morcillo S Macias-Gonzalez M - - 20301485 + + 31462513 PubMed - Familial Lipoprotein Lipase Deficiency - - 1993 - Burnett JR - Hooper AJ - Hegele RA + Identification of ApoA4 as a sphingosine 1-phosphate chaperone in ApoM- and albumin-deficient mice. + J Lipid Res + 2019 + Obinata H + Kuo A + Wada Y + Swendeman S + Liu CH + Blaho VA + Nagumo R + Satoh K + Izumi T + Hla T + + + 28766509 + PubMed + High-density lipoprotein metabolism and reverse cholesterol transport: strategies for raising HDL cholesterol. + Anatol J Cardiol + 2017 + Tosheska Trajkovska K + Topuzovska S + + + familial hyperlipidemia + DOID:1168 + Disease + + + 27457486 + PubMed + APOE genotype and stress response - a mini review. + Lipids Health Dis + 2016 + Dose J + Huebbe P + Nebel A + Rimbach G + + + 31676439 + PubMed + Interleukin 10 promotes macrophage uptake of HDL and LDL bystimulating fluid-phase endocytosis. + Biochim Biophys Acta Mol Cell Biol Lipids + 2020 + Lucero D + Islam P + Freeman LA + Jin X + Pryor M + Tang J + Kruth HS + Remaley AT 23055695 @@ -783,18 +808,6 @@ Goldberg AS Hegele RA - - 28882953 - PubMed - <i>SCARB1</i>Gene Polymorphisms and HDL Subfractions in Coronary Artery Disease. - In Vivo - 2017 - Ayhan H - Gormus U - Isbir S - Yilmaz SG - Isbir T - 22474067 PubMed @@ -810,33 +823,20 @@ Bonnet J Lagrost L - - 27457486 - PubMed - APOE genotype and stress response - a mini review. - Lipids Health Dis - 2016 - Dose J - Huebbe P - Nebel A - Rimbach G - - - 14592533 - PubMed - The role of scavenger receptor class B type I (SR-BI) in lipid trafficking. defining the rules for lipid traders. - Int J Biochem Cell Biol - 2004 - Rhainds D - Brissette L - - - 26247089 + + 32120838 PubMed - Introduction to Lipids and Lipoproteins - - 2000 - Feingold KR + Association between the<i>APOA2</i>rs3813627 Single Nucleotide Polymorphism and HDL and APOA1 Levels Through BMI. + Biomedicines + 2020 + Boughanem H + Bandera-Merchán B + Hernández-Alonso P + Moreno-Morales N + Tinahones FJ + Lozano J + Morcillo S + Macias-Gonzalez M 28766509 @@ -847,27 +847,27 @@ Tosheska Trajkovska K Topuzovska S - - disease pathway - PW:0000013 - Pathway Ontology - - - 31462513 + + 29100061 PubMed - Identification of ApoA4 as a sphingosine 1-phosphate chaperone in ApoM- and albumin-deficient mice. - J Lipid Res - 2019 - Obinata H - Kuo A - Wada Y - Swendeman S - Liu CH - Blaho VA - Nagumo R - Satoh K - Izumi T - Hla T + Apolipoprotein C-II: New findings related to genetics, biochemistry, and role in triglyceride metabolism. + Atherosclerosis + 2017 + Wolska A + Dunbar RL + Freeman LA + Ueda M + Amar MJ + Sviridov DO + Remaley AT + + + 25328986 + PubMed + Apolipoprotein E isoforms and lipoprotein metabolism. + IUBMB Life + 2014 + Phillips MC diff --git a/pathways/WP5110/WP5110.json b/pathways/WP5110/WP5110.json index a95c5bb24..8b24f27a7 100644 --- a/pathways/WP5110/WP5110.json +++ b/pathways/WP5110/WP5110.json @@ -4327,7 +4327,7 @@ "id": "publicationXrefb34", "source": "Drug Des Devel Ther", "standardName": "Cholesteryl ester transfer protein inhibitors for dyslipidemia: focus on dalcetrapib.", - "textContent": "7", + "textContent": "6", "type": [ "PublicationXref", "PubMed:23055695" @@ -4376,7 +4376,7 @@ "id": "publicationXrefb52", "source": "J Lipid Res", "standardName": "Identification of ApoA4 as a sphingosine 1-phosphate chaperone in ApoM- and albumin-deficient mice.", - "textContent": "25", + "textContent": "26", "type": [ "PublicationXref", "PubMed:31462513" @@ -4394,7 +4394,7 @@ "id": "publicationXrefb79", "source": "Anatol J Cardiol", "standardName": "High-density lipoprotein metabolism and reverse cholesterol transport: strategies for raising HDL cholesterol.", - "textContent": "21", + "textContent": "20", "type": [ "PublicationXref", "PubMed:28766509" @@ -4412,7 +4412,7 @@ "id": "publicationXrefbab", "source": "Anatol J Cardiol", "standardName": "High-density lipoprotein metabolism and reverse cholesterol transport: strategies for raising HDL cholesterol.", - "textContent": "17", + "textContent": "19", "type": [ "PublicationXref", "PubMed:28766509" @@ -4473,7 +4473,7 @@ "id": "publicationXrefc65", "source": "J Lipid Res", "standardName": "N-terminal mutation of apoA-I and interaction with ABCA1 reveal mechanisms of nascent HDL biogenesis.", - "textContent": "27", + "textContent": "25", "type": [ "PublicationXref", "PubMed:30249788" @@ -4518,7 +4518,7 @@ "id": "publicationXrefc81", "source": "In Vivo", "standardName": "SCARB1Gene Polymorphisms and HDL Subfractions in Coronary Artery Disease.", - "textContent": "20", + "textContent": "14", "type": [ "PublicationXref", "PubMed:28882953" @@ -4560,7 +4560,7 @@ "id": "publicationXrefc9f", "source": "Curr Opin Endocrinol Diabetes Obes", "standardName": "Familial dysbetalipoproteinemia: an underdiagnosed lipid disorder.", - "textContent": "14", + "textContent": "15", "type": [ "PublicationXref", "PubMed:28098593" @@ -4602,7 +4602,7 @@ "id": "publicationXrefd2a", "source": "Yale J Biol Med", "standardName": "Low-density lipoprotein receptor (LDLR) family orchestrates cholesterol homeostasis.", - "textContent": "6", + "textContent": "7", "type": [ "PublicationXref", "PubMed:22461740" @@ -4664,7 +4664,7 @@ "id": "publicationXrefd68", "source": "J Lipid Res", "standardName": "N-terminal mutation of apoA-I and interaction with ABCA1 reveal mechanisms of nascent HDL biogenesis.", - "textContent": "26", + "textContent": "27", "type": [ "PublicationXref", "PubMed:30249788" @@ -4682,7 +4682,7 @@ "id": "publicationXrefdd8", "source": "Int J Biochem Cell Biol", "standardName": "The role of scavenger receptor class B type I (SR-BI) in lipid trafficking. defining the rules for lipid traders.", - "textContent": "3", + "textContent": "4", "type": [ "PublicationXref", "PubMed:14592533" @@ -4745,7 +4745,7 @@ "id": "publicationXrefe5a", "source": "Nat Commun", "standardName": "Macrophage VLDLR mediates obesity-induced insulin resistance with adipose tissue inflammation.", - "textContent": "15", + "textContent": "17", "type": [ "PublicationXref", "PubMed:29057873" @@ -4763,7 +4763,7 @@ "id": "publicationXrefe79", "source": "Int J Biochem Cell Biol", "standardName": "The role of scavenger receptor class B type I (SR-BI) in lipid trafficking. defining the rules for lipid traders.", - "textContent": "4", + "textContent": "3", "type": [ "PublicationXref", "PubMed:14592533" @@ -4804,7 +4804,7 @@ "id": "publicationXrefeef", "source": "Atherosclerosis", "standardName": "Apolipoprotein C-II: New findings related to genetics, biochemistry, and role in triglyceride metabolism.", - "textContent": "18", + "textContent": "21", "type": [ "PublicationXref", "PubMed:29100061" @@ -4867,7 +4867,7 @@ "id": "publicationXreff4b", "source": "In Vivo", "standardName": "SCARB1Gene Polymorphisms and HDL Subfractions in Coronary Artery Disease.", - "textContent": "19", + "textContent": "18", "type": [ "PublicationXref", "PubMed:28882953" diff --git a/pathways/WP710/WP710.gpml b/pathways/WP710/WP710.gpml index 78520152d..f73476069 100644 --- a/pathways/WP710/WP710.gpml +++ b/pathways/WP710/WP710.gpml @@ -1325,51 +1325,6 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - 17768402 - PubMed - Emergence of a DNA-damage response network consisting of Fanconi anaemia and BRCA proteins. - Nat Rev Genet - 2007 - Wang W - - - 14634621 - PubMed - The Bcl-2 family: roles in cell survival and oncogenesis. - Oncogene - 2003 - Cory S - Huang DC - Adams JM - - - 17060944 - PubMed - Polycomb silencers control cell fate, development and cancer. - Nat Rev Cancer - 2006 - Sparmann A - van Lohuizen M - - - 16921403 - PubMed - Regulation of the INK4b-ARF-INK4a tumour suppressor locus: all for one or one for all. - Nat Rev Mol Cell Biol - 2006 - Gil J - Peters G - - - 15545627 - PubMed - Living with or without cyclins and cyclin-dependent kinases. - Genes Dev - 2004 - Sherr CJ - Roberts JM - 19111245 PubMed @@ -1382,20 +1337,15 @@ Proteins on this pathway have targeted assays available via the [https://assays. Castadot P Magnأ¯آ؟آ½أ¯آ؟آ½أژآ© N - - 15688066 + + 16805667 PubMed - p53: traffic cop at the crossroads of DNA repair and recombination. - Nat Rev Mol Cell Biol - 2005 - Sengupta S - Harris CC + Surviving the breakup: the DNA damage checkpoint. + Annu Rev Genet + 2006 + Harrison JC + Haber JE - - p53-dependent G1/S DNA damage checkpoint pathway - PW:0000303 - Pathway Ontology - 15339658 PubMed @@ -1405,32 +1355,32 @@ Proteins on this pathway have targeted assays available via the [https://assays. Pagano M Jackson PK - - 15668327 + + p53-dependent G1/S DNA damage checkpoint pathway + PW:0000303 + Pathway Ontology + + + p53 signaling pathway + PW:0000718 + Pathway Ontology + + + 15688066 PubMed - Chromosomal instability in oral cancer cells. - J Dent Res + p53: traffic cop at the crossroads of DNA repair and recombination. + Nat Rev Mol Cell Biol 2005 - Reshmi SC - Gollin SM - - - 17943134 - PubMed - The impact of a negligent G2/M checkpoint on genomic instability and cancer induction. - Nat Rev Cancer - 2007 - Lأ¯آ؟آ½أ¯آ؟آ½أژآ©brich M - Jeggo PA + Sengupta S + Harris CC - - 17380161 + + 15719025 PubMed - p53 in health and disease. - Nat Rev Mol Cell Biol - 2007 - Vousden KH - Lane DP + The role of BH3-only proteins in the immune system. + Nat Rev Immunol + 2005 + Strasser A 14993903 @@ -1441,6 +1391,28 @@ Proteins on this pathway have targeted assays available via the [https://assays. Zhou BB Bartek J + + 15545627 + PubMed + Living with or without cyclins and cyclin-dependent kinases. + Genes Dev + 2004 + Sherr CJ + Roberts JM + + + 20610534 + PubMed + Beta-catenin (CTNNB1) promotes preovulatory follicular development but represses LH-mediated ovulation and luteinization. + Mol Endocrinol + 2010 + Fan HY + O'Connor A + Shitanaka M + Shimada M + Liu Z + Richards JS + 18004398 PubMed @@ -1452,22 +1424,23 @@ Proteins on this pathway have targeted assays available via the [https://assays. Collins I Garrett MD - - 16805667 + + 17568790 PubMed - Surviving the breakup: the DNA damage checkpoint. - Annu Rev Genet - 2006 - Harrison JC - Haber JE + CDC25 phosphatases in cancer cells: key players? Good targets? + Nat Rev Cancer + 2007 + Boutros R + Lobjois V + Ducommun B - - 15719025 + + 17768402 PubMed - The role of BH3-only proteins in the immune system. - Nat Rev Immunol - 2005 - Strasser A + Emergence of a DNA-damage response network consisting of Fanconi anaemia and BRCA proteins. + Nat Rev Genet + 2007 + Wang W 15343279 @@ -1478,33 +1451,60 @@ Proteins on this pathway have targeted assays available via the [https://assays. Ljungman M Lane DP - - 20610534 + + 14634621 PubMed - Beta-catenin (CTNNB1) promotes preovulatory follicular development but represses LH-mediated ovulation and luteinization. - Mol Endocrinol - 2010 - Fan HY - O'Connor A - Shitanaka M - Shimada M - Liu Z - Richards JS + The Bcl-2 family: roles in cell survival and oncogenesis. + Oncogene + 2003 + Cory S + Huang DC + Adams JM - - p53 signaling pathway - PW:0000718 - Pathway Ontology - - - 17568790 + + 15668327 PubMed - CDC25 phosphatases in cancer cells: key players? Good targets? + Chromosomal instability in oral cancer cells. + J Dent Res + 2005 + Reshmi SC + Gollin SM + + + 17380161 + PubMed + p53 in health and disease. + Nat Rev Mol Cell Biol + 2007 + Vousden KH + Lane DP + + + 17060944 + PubMed + Polycomb silencers control cell fate, development and cancer. + Nat Rev Cancer + 2006 + Sparmann A + van Lohuizen M + + + 16921403 + PubMed + Regulation of the INK4b-ARF-INK4a tumour suppressor locus: all for one or one for all. + Nat Rev Mol Cell Biol + 2006 + Gil J + Peters G + + + 17943134 + PubMed + The impact of a negligent G2/M checkpoint on genomic instability and cancer induction. Nat Rev Cancer 2007 - Boutros R - Lobjois V - Ducommun B + Lأ¯آ؟آ½أ¯آ؟آ½أژآ©brich M + Jeggo PA diff --git a/pathways/WP710/WP710.json b/pathways/WP710/WP710.json index d7b7dee62..6b615d6d4 100644 --- a/pathways/WP710/WP710.json +++ b/pathways/WP710/WP710.json @@ -13326,7 +13326,7 @@ "id": "publicationXrefa1b", "source": "Nat Rev Mol Cell Biol", "standardName": "p53 in health and disease.", - "textContent": "14", + "textContent": "15", "type": [ "PublicationXref", "PubMed:17380161" @@ -13381,7 +13381,7 @@ "id": "publicationXrefaf9", "source": "Cell", "standardName": "Wagging the dogma; tissue-specific cell cycle control in the mouse embryo.", - "textContent": "3", + "textContent": "2", "type": [ "PublicationXref", "PubMed:15339658" @@ -13399,7 +13399,7 @@ "id": "publicationXrefb66", "source": "Nat Rev Cancer", "standardName": "The impact of a negligent G2/M checkpoint on genomic instability and cancer induction.", - "textContent": "13", + "textContent": "16", "type": [ "PublicationXref", "PubMed:17943134" @@ -13417,7 +13417,7 @@ "id": "publicationXrefbf4", "source": "J Dent Res", "standardName": "Chromosomal instability in oral cancer cells.", - "textContent": "7", + "textContent": "8", "type": [ "PublicationXref", "PubMed:15668327" @@ -13435,7 +13435,7 @@ "id": "publicationXrefc04", "source": "Nat Rev Cancer", "standardName": "Polycomb silencers control cell fate, development and cancer.", - "textContent": "9", + "textContent": "10", "type": [ "PublicationXref", "PubMed:17060944" @@ -13473,7 +13473,7 @@ "id": "publicationXrefc56", "source": "Nat Rev Cancer", "standardName": "CHK2 kinase: cancer susceptibility and cancer therapy - two sides of the same coin?", - "textContent": "15", + "textContent": "12", "type": [ "PublicationXref", "PubMed:18004398" @@ -13513,7 +13513,7 @@ "id": "publicationXrefd50", "source": "Annu Rev Genet", "standardName": "Surviving the breakup: the DNA damage checkpoint.", - "textContent": "11", + "textContent": "9", "type": [ "PublicationXref", "PubMed:16805667" @@ -13552,7 +13552,7 @@ "id": "publicationXrefda1", "source": "Genes Dev", "standardName": "Living with or without cyclins and cyclin-dependent kinases.", - "textContent": "2", + "textContent": "4", "type": [ "PublicationXref", "PubMed:15545627" @@ -13570,7 +13570,7 @@ "id": "publicationXrefdab", "source": "Nat Rev Mol Cell Biol", "standardName": "Regulation of the INK4b-ARF-INK4a tumour suppressor locus: all for one or one for all.", - "textContent": "10", + "textContent": "11", "type": [ "PublicationXref", "PubMed:16921403" @@ -13587,7 +13587,7 @@ "id": "publicationXrefdf4", "source": "Nat Rev Genet", "standardName": "Emergence of a DNA-damage response network consisting of Fanconi anaemia and BRCA proteins.", - "textContent": "12", + "textContent": "14", "type": [ "PublicationXref", "PubMed:17768402" @@ -13606,7 +13606,7 @@ "id": "publicationXrefe48", "source": "Nat Rev Cancer", "standardName": "CDC25 phosphatases in cancer cells: key players? Good targets?", - "textContent": "16", + "textContent": "13", "type": [ "PublicationXref", "PubMed:17568790" @@ -13623,7 +13623,7 @@ "id": "publicationXrefe6f", "source": "Nat Rev Immunol", "standardName": "The role of BH3-only proteins in the immune system.", - "textContent": "8", + "textContent": "7", "type": [ "PublicationXref", "PubMed:15719025" @@ -13641,7 +13641,7 @@ "id": "publicationXrefefb", "source": "Nat Rev Cancer", "standardName": "Targeting the checkpoint kinases: chemosensitization versus chemoprotection.", - "textContent": "4", + "textContent": "3", "type": [ "PublicationXref", "PubMed:14993903"