From 7cb72593b7b7b58d45df64dc17a6d81e87bfc2a8 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Thu, 5 Sep 2024 02:45:59 +0000 Subject: [PATCH] Process GPML changes --- pathways/WP4010/WP4010.gpml | 310 ++++++++++++++++++------------------ pathways/WP54/WP54.gpml | 215 +++++++++++++------------ pathways/WP67/WP67.gpml | 168 +++++++++++-------- 3 files changed, 364 insertions(+), 329 deletions(-) diff --git a/pathways/WP4010/WP4010.gpml b/pathways/WP4010/WP4010.gpml index e572fcbf90..45bee2c263 100644 --- a/pathways/WP4010/WP4010.gpml +++ b/pathways/WP4010/WP4010.gpml @@ -1,5 +1,5 @@ - + This liver steatosis AOP starts from the top with different molecular initiating events going down towards liver steatosis. The black nodes are Key Events and green nodes are molecular pathways. Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocytes, caused either by over-nutrition, visceral obesity, metabolic syndrome, or environmental toxins. Liver steatosis can be divided into three main categories: alcoholic liver disease (ALD), non-alcoholic liver disease (NAFLD), and toxicant-associated liver disease (TAFLD).[https://pubmed.ncbi.nlm.nih.gov/28210688/ Review on liver steatosis] @@ -21,7 +21,7 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - + @@ -41,7 +41,7 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - + @@ -57,7 +57,7 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - + @@ -121,7 +121,7 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - + @@ -133,7 +133,7 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - + @@ -260,15 +260,15 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - - + + - - + + @@ -324,15 +324,15 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - + - - + + @@ -370,8 +370,8 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - - + + @@ -413,16 +413,16 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - - - + + + - - + + @@ -583,14 +583,14 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - + - - + + @@ -613,73 +613,37 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt - - 15581595 - PubMed - Regulatory network of lipid-sensing nuclear receptors: roles for CAR, PXR, LXR, and FXR. - Arch Biochem Biophys - 2005 - Handschin C - Meyer UA - - - 15340055 - PubMed - Nuclear receptors CAR and PXR cross talk with FOXO1 to regulate genes that encode drug-metabolizing and gluconeogenic enzymes - Mol Cell Biol - 2004 - Kodama S - - - 15004031 - PubMed - The nuclear receptor CAR is a regulator of thyroid hormone metabolism during caloric restriction. - J Biol Chem - 2004 - Maglich JM - Watson J - McMillen PJ - Goodwin B - Willson TM - Moore JT - - - 1844873 - PubMed - Human AH locus polymorphism and cancer: inducibility of CYP1A1 and other genes by combustion products and dioxin. - Pharmacogenetics - 1991 - Nebert DW - Petersen DD - Puga A - - - 18288955 + + 11343253 PubMed - Xenobiotic-induced transcriptional regulation of xenobiotic metabolizing enzymes of the cytochrome P450 superfamily in human extrahepatic tissues. - Curr Drug Metab - 2008 - Pavek P - Dvorak Z + The phenobarbital response enhancer module in the human bilirubin UDP-glucuronosyltransferase UGT1A1 gene and regulation by the nuclear receptor CAR. + Hepatology + 2001 + Sugatani J + Kojima H + Ueda A + Kakizaki S + Yoshinari K + Gong QH + Owens IS + Negishi M + Sueyoshi T - - 21420387 + + fatty liver disease + DOID:9452 + Disease + + + 10398686 PubMed - From differential induction of UDP-glucuronosyltransferases in rat liver to characterization of responsible ligand-activated transcription factors, and their multilevel crosstalk in humans. - Biochem Pharmacol - 2011 - Bock KW - - - 9789279277443 - ISBN - Description of Prototype Modes-of-Action Related to Repeated Dose Toxicity - http://publications.jrc.ec.europa.eu/repository/bitstream/JRC75689/lb-na-25631-en-n.pdf - 2012 - Brigitte Landesmann - Marina Goumenou - Sharon Munn - Maurice Whelan + p27(Kip1) induction and inhibition of proliferation by the intracellular Ah receptor in developing thymus and hepatoma cells. + Genes Dev + 1999 + Kolluri SK + Weiss C + Koff A + Göttlicher M 12611900 @@ -699,15 +663,6 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt Willson TM Moore JT - - 15581595 - PubMed - Regulatory network of lipid-sensing nuclear receptors: roles for CAR, PXR, LXR, and FXR. - Arch Biochem Biophys - 2005 - Handschin C - Meyer UA - 8120057 PubMed @@ -737,47 +692,25 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt Dai X Evers R - - fatty liver disease - DOID:9452 - Disease - - - 11343253 - PubMed - The phenobarbital response enhancer module in the human bilirubin UDP-glucuronosyltransferase UGT1A1 gene and regulation by the nuclear receptor CAR. - Hepatology - 2001 - Sugatani J - Kojima H - Ueda A - Kakizaki S - Yoshinari K - Gong QH - Owens IS - Negishi M - Sueyoshi T - - - 10398686 + + 15340055 PubMed - p27(Kip1) induction and inhibition of proliferation by the intracellular Ah receptor in developing thymus and hepatoma cells. - Genes Dev - 1999 - Kolluri SK - Weiss C - Koff A - Göttlicher M + Nuclear receptors CAR and PXR cross talk with FOXO1 to regulate genes that encode drug-metabolizing and gluconeogenic enzymes + Mol Cell Biol + 2004 + Kodama S - - 26451809 + + 11502724 PubMed - The identification of nuclear receptors associated with hepatic steatosis to develop and extend adverse outcome pathways. - Crit Rev Toxicol - 2016 - Mellor CL - Steinmetz FP - Cronin MT + Metabolic activation of polycyclic aromatic hydrocarbons and other procarcinogens by cytochromes P450 1A1 and P450 1B1 allelic variants and other human cytochromes P450 in Salmonella typhimurium NM2009. + Drug Metab Dispos + 2001 + Shimada T + Oda Y + Gillam EM + Guengerich FP + Inoue K 8910454 @@ -793,18 +726,22 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt Sutter TR Greenlee WF - - 11502724 - PubMed - Metabolic activation of polycyclic aromatic hydrocarbons and other procarcinogens by cytochromes P450 1A1 and P450 1B1 allelic variants and other human cytochromes P450 in Salmonella typhimurium NM2009. - Drug Metab Dispos - 2001 - Shimada T - Oda Y - Gillam EM - Guengerich FP - Inoue K + + 9789279277443 + ISBN + Description of Prototype Modes-of-Action Related to Repeated Dose Toxicity + http://publications.jrc.ec.europa.eu/repository/bitstream/JRC75689/lb-na-25631-en-n.pdf + 2012 + Brigitte Landesmann + Marina Goumenou + Sharon Munn + Maurice Whelan + + disease pathway + PW:0000013 + Pathway Ontology + 17595319 PubMed @@ -818,16 +755,42 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt De La Cruz IJ Chatterjee B - - disease pathway - PW:0000013 - Pathway Ontology - - - hepatocyte - CL:0000182 - Cell Type - + + 26451809 + PubMed + The identification of nuclear receptors associated with hepatic steatosis to develop and extend adverse outcome pathways. + Crit Rev Toxicol + 2016 + Mellor CL + Steinmetz FP + Cronin MT + + + 15581595 + PubMed + Regulatory network of lipid-sensing nuclear receptors: roles for CAR, PXR, LXR, and FXR. + Arch Biochem Biophys + 2005 + Handschin C + Meyer UA + + + 21420387 + PubMed + From differential induction of UDP-glucuronosyltransferases in rat liver to characterization of responsible ligand-activated transcription factors, and their multilevel crosstalk in humans. + Biochem Pharmacol + 2011 + Bock KW + + + 15581595 + PubMed + Regulatory network of lipid-sensing nuclear receptors: roles for CAR, PXR, LXR, and FXR. + Arch Biochem Biophys + 2005 + Handschin C + Meyer UA + 16873678 PubMed @@ -843,6 +806,43 @@ Adverse outcome pathway liver steatosis; the accumulation of lipids in hepatocyt Girard J Postic C + + 1844873 + PubMed + Human AH locus polymorphism and cancer: inducibility of CYP1A1 and other genes by combustion products and dioxin. + Pharmacogenetics + 1991 + Nebert DW + Petersen DD + Puga A + + + 15004031 + PubMed + The nuclear receptor CAR is a regulator of thyroid hormone metabolism during caloric restriction. + J Biol Chem + 2004 + Maglich JM + Watson J + McMillen PJ + Goodwin B + Willson TM + Moore JT + + + 18288955 + PubMed + Xenobiotic-induced transcriptional regulation of xenobiotic metabolizing enzymes of the cytochrome P450 superfamily in human extrahepatic tissues. + Curr Drug Metab + 2008 + Pavek P + Dvorak Z + + + hepatocyte + CL:0000182 + Cell Type + 21908933 PubMed diff --git a/pathways/WP54/WP54.gpml b/pathways/WP54/WP54.gpml index e9858bb7da..f6dacc46f0 100644 --- a/pathways/WP54/WP54.gpml +++ b/pathways/WP54/WP54.gpml @@ -1,184 +1,182 @@ - - - Based on http://pathway.yeastgenome.org/biocyc/ - - - - - - + + - + - + - - - - - - - - + + + + - - - + + + - - - + + + + + + + - - - + + + + + + + - - - + + + - - - + + + + + + + + + + + - - + + + - + - - + + - + - - - + + + + + + + + + - - + + + - + - - + + - + - - + + + - - - - - + + + + - - - - - + + + + + - - - - - + + + + - - - - - + + + + - - - - + + + + - - - - - + + + + - - - - - - - - - + diff --git a/pathways/WP67/WP67.gpml b/pathways/WP67/WP67.gpml index c8c98aadcc..6c56fbbf24 100644 --- a/pathways/WP67/WP67.gpml +++ b/pathways/WP67/WP67.gpml @@ -1,105 +1,133 @@ - + The first five steps of arginine biosynthesis in S. cerevisiae take place in the mitochondrion (CITS: [11553611])(CITS: [Hinnebusch]). This part of the pathway is known as the acetylated derivatives cycle because the acetyl group that is added to L-glutamate in the first step of the pathway is recycled via N-acetylglutamate generated in the fifth step. The enzymes that catalyze the second and third steps are encoded by a single gene (ARG5,6) that is translated into a pre-protein which is imported into mitochondria and cleaved there to yield two enzymes, N-acetylglutamate kinase and N-acetylglutamyl-phosphate reductase (CITS: [1649049]). These enzymes form a complex with each other and with N-acetylglutamate synthase, the first enzyme in the pathway, which may have implications for regulation of their activity (CITS: [11553611]). The mitochondrial steps of the arginine biosynthesis pathway result in the formation of ornithine, which is exported to the cytoplasm by the transporter Ort1p (CITS: [8798783]). In the cytoplasm, L-ornithine is converted to L-arginine in three reactions mediated by ornithine carbamoyltransferase, arginosuccinate synthase, and argininosuccinate lyase. Transcription of genes of the arginine biosynthetic pathway, as well as of other amino acid biosynthetic pathways, is activated by the transcription factor Gcn4p under conditions of amino acid starvation (CITS: [11390663])(CITS: [Hinnebusch]). Transcription of ARG1, ARG3, ARG5,6, and ARG8 is also repressed in the presence of arginine by the ArgR/Mcm1p complex, which consists of Arg80p, Arg81p, Arg82p, and Mcm1p (CITS: [14563547]). The transcriptional activator Gcn4p interacts with subunits of the ArgR/Mcm1p repressor, allowing for fine-tuning of transcriptional control in response to arginine availability (CITS: [15289616]). SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html - Based on http://pathway.yeastgenome.org/biocyc/ - - - - + d39 + + + + + - - - + + + - - - + + + - - - + + + + - - - + + + - - - - + + + + + + + + + + + - + - + - + + + + + + + + + - + - - - - - - + - - - + + + - - + + - - - - - - - - - - - - - + + + + + + + + - - + + + + + + + + + - - + + + - - - - - + + + + + - - - - - + + + + - - + + + + + + + + + + + + + + + + @@ -107,5 +135,13 @@ SOURCE: SGD pathways, http://pathway.yeastgenome.org/server.html PW:0001083 Pathway Ontology + + + PubMed + + https://pathway.yeastgenome.org/YEAST/NEW-IMAGE?type=PATHWAY&object=ASPARAGINE-BIOSYNTHESIS-1 + + +