diff --git a/pathways/WP2456/WP2456.gpml b/pathways/WP2456/WP2456.gpml index 141e7e129e..c19413a85e 100644 --- a/pathways/WP2456/WP2456.gpml +++ b/pathways/WP2456/WP2456.gpml @@ -1,6 +1,6 @@ - - Hypoxia-inducible factor 1A and peroxisome proliferator activated receptor gamma play a role in regulating glycolysis. + + The genes hypoxia-inducible factor 1A and peroxisome proliferator activated receptor gamma play a role in regulating glycolysis, triacylglyceride synthesis, and ultimately hypertrophic cardiomyopathy. This diagram is derived from figure 6D in [https://pubmed.ncbi.nlm.nih.gov/19490906/ PMID 19490906]: @@ -8,248 +8,442 @@ This diagram is derived from figure 6D in [https://pubmed.ncbi.nlm.nih.gov/19490 This pathway is part the [https://assays.cancer.gov/available_assays?wp_id=WP2456 CPTAC Assay Portal]. b8b - + + + + + + + + + - + - + - + + + + + - + - - - - - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - - + + - - + + - - - + + + + - - - + + + + + + + + + + + - - - + + + - - - + + + - - + + - - + + - - + + - - - + + + - - - + + + - - + + - - + + - - + + - - + + - - - + + + + - - + + - - + + - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + - - + + + + + + + + + + + + + + + + + + + + cardiac muscle cell + CL:0000746 + Cell Type + 19490906 PubMed @@ -281,6 +475,16 @@ This pathway is part the [https://assays.cancer.gov/available_assays?wp_id=WP245 PW:0000004 Pathway Ontology + + lipid metabolic pathway + PW:0000010 + Pathway Ontology + + + hypertrophic cardiomyopathy + DOID:11984 + Disease + diff --git a/pathways/WP3645/WP3645.gpml b/pathways/WP3645/WP3645.gpml index 34622f7fb8..215dbbf4a7 100644 --- a/pathways/WP3645/WP3645.gpml +++ b/pathways/WP3645/WP3645.gpml @@ -1,12 +1,12 @@ - + NAD+ biosynthetic pathways. NAD+ levels are maintained by three independent pathways. First, the Preiss-Handler pathway uses dietary nicotinic acid and the enzyme nicotinic acid phosphoribosyltransferase (NAPRT) to generate NAMN, which is then transformed into NAAD by NAMN transferase (NMNAT). Three forms of this enzyme (NMNAT1, -2, and -3) have distinct subcellular localizations. The process is completed by the transformation of NAAD into NAD+ by NAD+ synthase (NADS). Second, the de novo synthesis pathway of NAD from tryptophan occurs through the kinurenine pathway (5). The first step in this pathway is the rate-limiting conversion of tryptophan to N-formylkinurenine (N-formylkin) by either IDO or TDO. Formylkinurenine is transformed into L-kinurenine (L-kin), 3-hydroxykinurenine, and 3-hydroxyanthranilic acid (3-HAA) and finally to ACMS. This compound can spontaneously condense and rearrange into quinolinic acid, which is transformed into NAMN, at which point it converges with the Preiss-Handler pathway. ACMS can also be decarboxylated into AMS by ACMS decarboxylase (ACMSD), leading to its oxidation into acetyl-CoA via the TCA cycle. Third, the NAD+ salvage pathway recycles the nicotinamide generated as a by-product of the enzymatic activities of NAD+-consuming enzymes: sirtuins, PARPs, and the cADPR synthases (CD38 and CD157). Initially, NAMPT recycles nicotinamide into NMN, which is then converted into NAD+ via the different NMNATs. Proteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP3645 CPTAC Assay Portal] ccb d27 - + @@ -169,220 +169,220 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - + + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - - + + + - - + + - - + + @@ -420,9 +420,23 @@ Proteins on this pathway have targeted assays available via the [https://assays. - + + + nicotinamide adenine dinucleotide biosynthesis, the salvage pathway + PW:0001375 + Pathway Ontology + + + 18429699 + PubMed + Nicotinic acid, nicotinamide, and nicotinamide riboside: a molecular evaluation of NAD+ precursor vitamins in human nutrition. + Annu Rev Nutr + 2008 + Bogan KL + Brenner C + classic metabolic pathway PW:0000002 @@ -441,14 +455,6 @@ Proteins on this pathway have targeted assays available via the [https://assays. 2015 Verdin E - - 18429699 - PubMed - Nicotinic acid, nicotinamide, and nicotinamide riboside: a molecular evaluation of NAD+ precursor vitamins in human nutrition. - Annu Rev Nutr - 2008 - Bogan KL - Brenner C - + diff --git a/pathways/WP3874/WP3874.gpml b/pathways/WP3874/WP3874.gpml index 3f8bad9445..597ab36300 100644 --- a/pathways/WP3874/WP3874.gpml +++ b/pathways/WP3874/WP3874.gpml @@ -1,137 +1,140 @@ - + This pathway is modeled after Figure 9 in the article "Gremlin utilizes canonical and non-canonical TGFB signaling to induce lysyl oxidase (LOX) genes in human trabecular meshwork cells". Gremlin is enables the TGF-B signaling pathways to oversee LOX and LOXL proteins and also demonstrates that the non-canonical JNK1/2 complex, canonical SMAD, and P38 signaling pathways are involved in this pathway. TGF-B signaling is possible through Gremlin's ability to bock the BMP signaling pathway which inhibits TGF-B receptors. Proteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP3874 CPTAC Assay Portal] f2f - - - - - + - + - - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - - + + P38 + - - - - - - - - - - - - - - - - - - - - - - - + + + - + + + BMP + + + - + + + + + - + + + Grem + + + - + + + + + - + + + + + - + + + + + + + + + - + + + + + - + + + + + - + + + + + - + + + + + - + - + - + + + + + + TGF-Beta + + + + Phosphate - - Phosphate + - + Phosphate @@ -148,122 +151,122 @@ Proteins on this pathway have targeted assays available via the [https://assays. - - + + - - - - + + + + - - - - + + + + - - - - - + + + + - - - - + + + + - - - - + + + + + - - - + + + - - - - + + + + + - - - - + + + + - - - - + + + + - - - - + + + + - - - - - + + + + - - - + + + - - - + + + - - - - - - + + + + + + - + @@ -278,11 +281,21 @@ Proteins on this pathway have targeted assays available via the [https://assays. + + Bone morphogenetic proteins signaling pathway + PW:0000330 + Pathway Ontology + primary angle-closure glaucoma DOID:1405 Disease + + trabecular meshwork cell + CL:0002367 + Cell Type + 23748100 PubMed @@ -293,16 +306,6 @@ Proteins on this pathway have targeted assays available via the [https://assays. Wordinger RJ Clark AF - - Bone morphogenetic proteins signaling pathway - PW:0000330 - Pathway Ontology - - - trabecular meshwork cell - CL:0002367 - Cell Type - diff --git a/pathways/WP5272/WP5272.gpml b/pathways/WP5272/WP5272.gpml index 4e7e1e291b..0e1f5ee64f 100644 --- a/pathways/WP5272/WP5272.gpml +++ b/pathways/WP5272/WP5272.gpml @@ -1,330 +1,349 @@ - + Electronegative LDL (LDL(-)) is a plasma LDL subfraction inducing induces cytokine release in monocytes by activating TLR4. The subsequent phosphorylation of p38 MAPK phosphorylation (which is higher compared to native LDL) through TLR4 and PI3k/Akt pathways activates NF-kB, AP-1 and CREB. These last three have a direct effect on four cytokines (IL1B, IL6, IL10 and MCP1), with bold black letters for the highest level of cytokine induction, gray letters for the lowest level and regular letter for the intermediate induction. d81 - - - + + + P38 MAPK (14) + - - + + P38 MAPK (12) + - - + + P38 MAPK (13) + - - + + P38 MAPK (11) + High content in Cer, Sph, NEFA - + - + - + aka Protein kinase B (PKB); Unknown if AKT1, AKT2, or AKT3 are meant in publication - + - + - + - + - - - - - - Phosphoinositide 3-kinases (PI3Ks), also called phosphatidylinositol 3-kinases, are a family of enzymes; paper doesn't mention which enzyme specifically is involved - - + + Phosphoinositide 3-kinases (PI3Ks), also called phosphatidylinositol 3-kinases, is a family of genes / enzymes. The paper does not mention which specifically is involved + + The structure of AP-1 is a heterodimer composed of proteins belonging to the c-Fos, c-Jun, ATF and JDP families; not specified in paper which one is meant. - + - - - - - - - - - - - - AKA MCP1 (alias) - + - + - + - + - + AKA MCP1(alias) - + - + - + - + - + AKA MCP1 (alias) - + AKA ATF4 - + - + - + - + - + - + - + - + - + - + - + - + + P38 MAPK (14) + + + + + P38 MAPK (13) + + + + + P38 MAPK (12) + + + + + P38 MAPK (11) + + + + - + - + - + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + + - - + @@ -7407,13 +7407,13 @@ Proteins on this pathway have targeted assays available via the [https://assays. - diff --git a/pathways/WP732/WP732.gpml b/pathways/WP732/WP732.gpml index 0d017ff8e3..678ad623b2 100644 --- a/pathways/WP732/WP732.gpml +++ b/pathways/WP732/WP732.gpml @@ -1,122 +1,122 @@ - + This pathway depicts the downstream signaling of serotonin via receptors 2A, 2B, and 2C, resulting in the activation of ELK-SRF and GATA4. Proteins on this pathway have targeted assays available via the [https://assays.cancer.gov/available_assays?wp_id=WP732 CPTAC Assay Portal] - + inositol 1,4,5-triphosphate receptor 1 - + - + - + v-raf-leukemia viral oncogene 1 - + - + ELK1, member of ETS oncogene family - + mitogen activated protein kinase 1 - + 5-hydroxytryptamine (serotonin) receptor 2C - + MAP kinase-activated protein kinase 2 - + mitogen activated protein kinase 3 - + 5-hydroxytryptamine (serotonin) receptor 2A - + GATA-binding protein 4/5/6 - + phospholipase C group - + mitogen activated protein kinase kinase 2 - + RAS protein-specific guanine nucleotide-releasing factor 1 - + - + mitogen activated protein kinase kinase 1 - + RAS guanyl releasing protein 1 - + 5-hydroxytryptamine (serotonin) receptor 2B - + - + ETS domain-containing protein Elk-4 (SRF accessory protein 1) - + guanine nucleotide binding protein, alpha q polypeptide - + 1,4,5-Insp3 - + serum response factor - + @@ -125,9 +125,9 @@ Proteins on this pathway have targeted assays available via the [https://assays. a65 - - - + + + @@ -156,8 +156,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. fc4 bc8 - - + + @@ -166,8 +166,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. b9f b26 - - + + @@ -187,8 +187,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. f1b e52 - - + + @@ -197,8 +197,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. c6c da6 - - + + @@ -212,8 +212,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. db7 d90 - - + + @@ -227,8 +227,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. b5f af0 - - + + @@ -239,8 +239,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. a8f - - + + @@ -266,8 +266,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. e3c b2c - - + + @@ -280,8 +280,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. f0d f29 - - + + @@ -291,8 +291,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. e1d - - + + @@ -302,8 +302,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. b3e - - + + @@ -313,8 +313,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. fd5 - - + + @@ -327,8 +327,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. ee5 ce8 - - + + @@ -341,8 +341,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. eca e5a - - + + @@ -355,8 +355,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. e54 cf9 - - + + @@ -385,8 +385,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. de4 cc7 - - + + @@ -408,8 +408,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. d53 e30 - - + + @@ -432,8 +432,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. c6f dc5 - - + + @@ -462,8 +462,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. f0c a9e - - + + @@ -476,8 +476,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. fbd c96 - - + + @@ -488,8 +488,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. c91 - - + + @@ -502,8 +502,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. f57 b08 - - + + @@ -534,8 +534,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. b1a e70 - - + + @@ -567,8 +567,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. ab2 c76 - - + + @@ -577,8 +577,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. ded c8b - - + + @@ -591,8 +591,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. d9e f92 - - + + @@ -612,8 +612,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. f33 fb3 - - + + @@ -637,8 +637,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. d60 cbf - - + + @@ -670,8 +670,8 @@ Proteins on this pathway have targeted assays available via the [https://assays. e07 c73 - - + + @@ -680,158 +680,135 @@ Proteins on this pathway have targeted assays available via the [https://assays. a28 b3a - - + + - - + + - - + + - - + + - - + + - - + + - - + + -