From aa8ffa38343a040b32e9de8961c7651ccf601fe5 Mon Sep 17 00:00:00 2001 From: GitHub Action Date: Wed, 19 Jul 2023 03:44:05 +0000 Subject: [PATCH] Process GPML changes --- pathways/WP4629/WP4629.gpml | 212 +++++++------- pathways/WP4806/WP4806.gpml | 534 +++++++++++++++++++----------------- 2 files changed, 379 insertions(+), 367 deletions(-) diff --git a/pathways/WP4629/WP4629.gpml b/pathways/WP4629/WP4629.gpml index c2e2f98d4c..23770f1bc7 100644 --- a/pathways/WP4629/WP4629.gpml +++ b/pathways/WP4629/WP4629.gpml @@ -1,5 +1,5 @@ - + Glycolysis is the metabolic pathway that converts glucose C6H12O6, into pyruvate, CH3COCOO- and H+. The free energy released in this process is used to form the ATP and NADH. This pathway was made during a research project at the UMCG, concerning changed glycolytic fluxes during the Warburg Effect. It is an extended version of the glycolysis pathway (WP534), and is descriptive of the content that is provided in the computer model of Shestov et al (2014). A second version, containing the content of the model itself as well as the corresponding supplement and article, can be found here [https://www.wikipathways.org/index.php/Pathway:WP4628] @@ -7,7 +7,7 @@ A second version, containing the content of the model itself as well as the corr This pathway was uploaded to provide a high resolution version to readers of the thesis. Description and pathway adapted from [https://www.wikipathways.org/index.php/Pathway:WP534] Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/25009227] - + @@ -27,11 +27,11 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + - + @@ -52,11 +52,11 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + - + @@ -66,12 +66,12 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 glucose-6-phosphate isomerase - + - + @@ -89,7 +89,7 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + @@ -115,13 +115,13 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + Type your comment here - + @@ -130,7 +130,7 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + @@ -143,12 +143,12 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + - + @@ -232,7 +232,7 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + @@ -244,7 +244,7 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + @@ -272,7 +272,7 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + @@ -297,47 +297,47 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + - - + + - - + + - + glucose-6-phosphate isomerase - + - - + + - - + + - + - + - - + + - + - + @@ -533,14 +533,14 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + - + @@ -567,13 +567,6 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - - - - - - - @@ -613,7 +606,7 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - + @@ -698,41 +691,34 @@ Referred article: Shestov et al., 2014 [https://www.ncbi.nlm.nih.gov/pubmed/2500 - - - - - - - - + - - + + - + - - + + - + - - + + - + - - + + - + - - + + diff --git a/pathways/WP4806/WP4806.gpml b/pathways/WP4806/WP4806.gpml index 7330805475..5206ee0a9e 100644 --- a/pathways/WP4806/WP4806.gpml +++ b/pathways/WP4806/WP4806.gpml @@ -1,20 +1,20 @@ - + Tyrosine kinase inhibitors (TKIs) are drugs that inhibit the phosphorylation, and subsequent activation, of tyrosine kinases. TKIs are typically used as cancer therapeutics, but development of resistance to TKIs in cancers is common. This pathway describes several mechanisms of TKI resistance in the context of EGFR signaling. Epidermal Growth Factor Receptor, EGFR, is a transmembrane tyrosine kinase that binds to the EGF-family of ligands. It activates several downstream signaling cascades, including MAPK, and leads to DNA synthesis and cell proliferation. Mutations and over-expression in EGFR is implicated in many cancers. The section of the pathway outlined in pink corresponds to mechanisms of TKI resistance. This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KEGG]. - + - + - + @@ -48,7 +48,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -60,18 +60,18 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + - + - + @@ -181,7 +181,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -234,7 +234,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -258,15 +258,15 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + - + - + @@ -274,7 +274,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -331,62 +331,62 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + - + - + - + - + - + - + - + - + - + - + - + @@ -394,11 +394,11 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + - + @@ -431,22 +431,22 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + - + - + - + @@ -454,17 +454,17 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + b94 - + parentid=P24385; parentsymbol=CCND1; site=EEVDLACtPtDVRDV; position=thr286; sitegrpid=447839; ptm=p; direction=d - + @@ -485,6 +485,16 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE + + parentid=P23458; parentsymbol=JAK1; site=IEtDkEyytVkDDRD; position=tyr1035; sitegrpid=448452; ptm=p; direction=u + + + + + parentid=P23458; parentsymbol=JAK1; site=AIEtDkEyytVkDDR; position=tyr1034; sitegrpid=448451; ptm=p; direction=u + + + f79 @@ -501,19 +511,19 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE parentid=P21860; parentsymbol=ERBB2; site=CPAsEQGyEEMRAFQ; position=tyr1289; sitegrpid=449858; ptm=p; direction=u - + T790M d09 - + T790M d09 - + @@ -528,7 +538,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE a1c - + @@ -541,6 +551,16 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE + + parentid=O60674; parentsymbol=JAK2; site=VLPQDKEyyKVkEPG; position=tyr1007; sitegrpid=448407; ptm=p; direction=u + + + + + parentid=O60674; parentsymbol=JAK2; site=LPQDKEyyKVkEPGE; position=tyr1008; sitegrpid=448408; ptm=p; direction=u + + + parentid=P40763; parentsymbol=STAT3; site=DPGsAAPyLKtKFIC; position=tyr705; sitegrpid=448192; ptm=p; direction=u @@ -654,7 +674,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE G469A, V600E, V599E d3d - + @@ -707,7 +727,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -754,7 +774,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -768,7 +788,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -781,22 +801,22 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - - + + - + - - + + @@ -816,7 +836,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -844,7 +864,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -865,7 +885,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -893,7 +913,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -949,7 +969,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -992,13 +1012,13 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + - + @@ -1006,7 +1026,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -1070,7 +1090,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -1113,7 +1133,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -1147,7 +1167,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -1161,43 +1181,43 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - - + + - + - - + + - - + + - - + + - - + + @@ -1225,14 +1245,14 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + - + @@ -1252,14 +1272,14 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - - + + - + @@ -1351,7 +1371,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -1365,7 +1385,7 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - + @@ -1500,71 +1520,9 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE - - 22426421 - PubMed - A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. - Nat Med - 2012 - Ng KP - Hillmer AM - Chuah CT - Juan WC - Ko TK - Teo AS - Ariyaratne PN - Takahashi N - Sawada K - Fei Y - Soh S - Lee WH - Huang JW - Allen JC Jr - Woo XY - Nagarajan N - Kumar V - Thalamuthu A - Poh WT - Ang AL - Mya HT - How GF - Yang LY - Koh LP - Chowbay B - Chang CT - Nadarajan VS - Chng WJ - Than H - Lim LC - Goh YT - Zhang S - Poh D - Tan P - Seet JE - Ang MK - Chau NM - Ng QS - Tan DS - Soda M - Isobe K - Nöthen MM - Wong TY - Shahab A - Ruan X - Cacheux-Rataboul V - Sung WK - Tan EH - Yatabe Y - Mano H - Soo RA - Chin TM - Lim WT - Ruan Y - Ong ST - - tyrosine-specific protein kinase mediated signaling pathway - PW:0001195 + altered growth factor signaling pathway + PW:0000298 Pathway Ontology @@ -1580,31 +1538,23 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE Zhang Z Halmos B - - 17463250 + + 25115383 PubMed - MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. - Science - 2007 - Engelman JA - Zejnullahu K - Mitsudomi T - Song Y - Hyland C - Park JO - Lindeman N - Gale CM - Zhao X - Christensen J - Kosaka T - Holmes AJ - Rogers AM - Cappuzzo F - Mok T - Lee C - Johnson BE - Cantley LC - Jänne PA + FGFR1 activation is an escape mechanism in human lung cancer cells resistant to afatinib, a pan-EGFR family kinase inhibitor. + Oncotarget + 2014 + Azuma K + Kawahara A + Sonoda K + Nakashima K + Tashiro K + Watari K + Izumi H + Kage M + Kuwano M + Ono M + Hoshino T 11397666 @@ -1616,11 +1566,24 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE Wikstrand CJ Bigner DD - - altered tyrosine-specific protein kinase mediated signaling pathway - PW:0001537 - Pathway Ontology - + + 19419954 + PubMed + Up-regulation of miR-21 by HER2/neu signaling promotes cell invasion. + J Biol Chem + 2009 + Huang TH + Wu F + Loeb GB + Hsu R + Heidersbach A + Brincat A + Horiuchi D + Lebbink RJ + Mo YY + Goga A + McManus MT + 22773810 PubMed @@ -1652,6 +1615,23 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE Ladanyi M Pao W + + tyrosine-specific protein kinase mediated signaling pathway + PW:0001195 + Pathway Ontology + + + altered tyrosine-specific protein kinase mediated signaling pathway + PW:0001537 + Pathway Ontology + + + + PubMed + + https://en.wikipedia.org/wiki/T790M + + 23404247 PubMed @@ -1680,6 +1660,59 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE Bardelli A Di Nicolantonio F + + 24535670 + PubMed + Reduced NF1 expression confers resistance to EGFR inhibition in lung cancer. + Cancer Discov + 2014 + de Bruin EC + Cowell C + Warne PH + Jiang M + Saunders RE + Melnick MA + Gettinger S + Walther Z + Wurtz A + Heynen GJ + Heideman DA + Gómez-Román J + García-Castaño A + Gong Y + Ladanyi M + Varmus H + Bernards R + Smit EF + Politi K + Downward J + + + 17463250 + PubMed + MET amplification leads to gefitinib resistance in lung cancer by activating ERBB3 signaling. + Science + 2007 + Engelman JA + Zejnullahu K + Mitsudomi T + Song Y + Hyland C + Park JO + Lindeman N + Gale CM + Zhao X + Christensen J + Kosaka T + Holmes AJ + Rogers AM + Cappuzzo F + Mok T + Lee C + Johnson BE + Cantley LC + Jänne PA + 23533263 PubMed @@ -1709,94 +1742,67 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE Bensinger SJ Mischel PS - - altered growth factor signaling pathway - PW:0000298 - Pathway Ontology - - - 11751408 - PubMed - Autocrine production of interleukin 6 causes multidrug resistance in breast cancer cells. - Cancer Res - 2001 - Conze D - Weiss L - Regen PS - Bhushan A - Weaver D - Johnson P - Rincón M - - - 25115383 - PubMed - FGFR1 activation is an escape mechanism in human lung cancer cells resistant to afatinib, a pan-EGFR family kinase inhibitor. - Oncotarget - 2014 - Azuma K - Kawahara A - Sonoda K - Nakashima K - Tashiro K - Watari K - Izumi H - Kage M - Kuwano M - Ono M - Hoshino T - - - 19419954 - PubMed - Up-regulation of miR-21 by HER2/neu signaling promotes cell invasion. - J Biol Chem - 2009 - Huang TH - Wu F - Loeb GB - Hsu R - Heidersbach A - Brincat A - Horiuchi D - Lebbink RJ - Mo YY - Goga A - McManus MT - - - 24535670 - PubMed - Reduced NF1 expression confers resistance to EGFR inhibition in lung cancer. - Cancer Discov - 2014 - de Bruin EC - Cowell C - Warne PH - Jiang M - Saunders RE - Melnick MA - Gettinger S - Walther Z - Wurtz A - Heynen GJ - Heideman DA - Gómez-Román J - García-Castaño A - Gong Y - Ladanyi M - Varmus H - Bernards R - Smit EF - Politi K - Downward J - - - + + 22426421 PubMed - - https://en.wikipedia.org/wiki/T790M - + A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. + Nat Med + 2012 + Ng KP + Hillmer AM + Chuah CT + Juan WC + Ko TK + Teo AS + Ariyaratne PN + Takahashi N + Sawada K + Fei Y + Soh S + Lee WH + Huang JW + Allen JC Jr + Woo XY + Nagarajan N + Kumar V + Thalamuthu A + Poh WT + Ang AL + Mya HT + How GF + Yang LY + Koh LP + Chowbay B + Chang CT + Nadarajan VS + Chng WJ + Than H + Lim LC + Goh YT + Zhang S + Poh D + Tan P + Seet JE + Ang MK + Chau NM + Ng QS + Tan DS + Soda M + Isobe K + Nöthen MM + Wong TY + Shahab A + Ruan X + Cacheux-Rataboul V + Sung WK + Tan EH + Yatabe Y + Mano H + Soo RA + Chin TM + Lim WT + Ruan Y + Ong ST 25984556 @@ -1816,6 +1822,20 @@ This pathway was based on [https://www.kegg.jp/kegg-bin/show_pathway?hsa01521 KE Zhao L Luu HH + + 11751408 + PubMed + Autocrine production of interleukin 6 causes multidrug resistance in breast cancer cells. + Cancer Res + 2001 + Conze D + Weiss L + Regen PS + Bhushan A + Weaver D + Johnson P + Rincón M +