From aa84229c5282e884c85aabbdd7edec68df521580 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 21 Jun 2023 14:03:16 -0400 Subject: [PATCH 1/9] fix: replace inaccurate GPR of MAR01527 and add new gene entries for several sodium channels --- model/Human-GEM.yml | 44 +++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 43 insertions(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 88682ac7..e4a6b2fc 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -226066,7 +226066,7 @@ - MAM02519e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100170 or ENSG00000105641 or ENSG00000198743" + - gene_reaction_rule: "ENSG00000007314 or ENSG00000102452 or ENSG00000136531 or ENSG00000136546 or ENSG00000138622 or ENSG00000144285 or ENSG00000162341 or ENSG00000164588 or ENSG00000168356 or ENSG00000169432 or ENSG00000183873 or ENSG00000185313 or ENSG00000186815 or ENSG00000196876" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" @@ -306876,6 +306876,9 @@ - !!omap - id: "ENSG00000007216" - name: "SLC13A2" + - !!omap + - id: "ENSG00000007314" + - name: "SCN4A" - !!omap - id: "ENSG00000007350" - name: "TKTL1" @@ -308346,6 +308349,9 @@ - !!omap - id: "ENSG00000102393" - name: "GLA" + - !!omap + - id: "ENSG00000102452" + - name: "NALCN" - !!omap - id: "ENSG00000102575" - name: "ACP5" @@ -310668,12 +310674,18 @@ - !!omap - id: "ENSG00000136521" - name: "NDUFB5" + - !!omap + - id: "ENSG00000136531" + - name: "SCN2A" - !!omap - id: "ENSG00000136536" - name: "MARCHF7" - !!omap - id: "ENSG00000136542" - name: "GALNT5" + - !!omap + - id: "ENSG00000136546" + - name: "SCN7A" - !!omap - id: "ENSG00000136628" - name: "EPRS1" @@ -310887,6 +310899,9 @@ - !!omap - id: "ENSG00000138621" - name: "PPCDC" + - !!omap + - id: "ENSG00000138622" + - name: "HCN4" - !!omap - id: "ENSG00000138641" - name: "HERC3" @@ -311400,6 +311415,9 @@ - !!omap - id: "ENSG00000144278" - name: "GALNT13" + - !!omap + - id: "ENSG00000144285" + - name: "SCN1A" - !!omap - id: "ENSG00000144290" - name: "SLC4A10" @@ -312411,6 +312429,9 @@ - !!omap - id: "ENSG00000162298" - name: "SYVN1" + - !!omap + - id: "ENSG00000162341" + - name: "TPCN2" - !!omap - id: "ENSG00000162365" - name: "CYP4A22" @@ -312690,6 +312711,9 @@ - !!omap - id: "ENSG00000164574" - name: "GALNT10" + - !!omap + - id: "ENSG00000164588" + - name: "HCN1" - !!omap - id: "ENSG00000164638" - name: "SLC29A4" @@ -313143,6 +313167,9 @@ - !!omap - id: "ENSG00000168350" - name: "DEGS2" + - !!omap + - id: "ENSG00000168356" + - name: "SCN11A" - !!omap - id: "ENSG00000168393" - name: "DTYMK" @@ -313233,6 +313260,9 @@ - !!omap - id: "ENSG00000169418" - name: "NPR1" + - !!omap + - id: "ENSG00000169432" + - name: "SCN9A" - !!omap - id: "ENSG00000169660" - name: "HEXD" @@ -314208,6 +314238,9 @@ - !!omap - id: "ENSG00000183828" - name: "NUDT14" + - !!omap + - id: "ENSG00000183873" + - name: "SCN5A" - !!omap - id: "ENSG00000183921" - name: "SDR42E2" @@ -314301,6 +314334,9 @@ - !!omap - id: "ENSG00000185274" - name: "GALNT17" + - !!omap + - id: "ENSG00000185313" + - name: "SCN10A" - !!omap - id: "ENSG00000185344" - name: "ATP6V0A2" @@ -314418,6 +314454,9 @@ - !!omap - id: "ENSG00000186792" - name: "HYAL3" + - !!omap + - id: "ENSG00000186815" + - name: "TPCN1" - !!omap - id: "ENSG00000186908" - name: "ZDHHC17" @@ -314601,6 +314640,9 @@ - !!omap - id: "ENSG00000196839" - name: "ADA" + - !!omap + - id: "ENSG00000196876" + - name: "SCN8A" - !!omap - id: "ENSG00000196950" - name: "SLC39A10" From d6ea247ac1c8a9edca465457dd771e79e984d737 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 21 Jun 2023 14:17:07 -0400 Subject: [PATCH 2/9] fix: added new rows to genes.tsv for new genes --- model/genes.tsv | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/model/genes.tsv b/model/genes.tsv index cb295fab..6cd89bd0 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2896,3 +2896,17 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000281500" "ENST00000525102;ENST00000330775;ENST00000357590;ENST00000538950;ENST00000545985;ENST00000526275;ENST00000532085;ENST00000650539;ENST00000527992;ENST00000638925;ENST00000638360;ENST00000638186;ENST00000530407;ENST00000524428;ENST00000525372;ENST00000525039;ENST00000529510;ENST00000532888;ENST00000526626;ENST00000525787;ENST00000534384" "ENSP00000476242;ENSP00000476176;ENSP00000475991;ENSP00000475241" "O43826" "SLC37A4" "" "Glucose-6-phosphate exchanger" "G6PT,G6PT1" "Endoplasmic reticulum" "SwissProt" "ENSG00000288702" "ENST00000482026" "ENSP00000418532" "P35503" "UGT1A3" "54659" "UDP glucuronosyltransferase family 1 member A3" "UGT1C" "Endoplasmic reticulum" "SwissProt" "ENSG00000288705" "ENST00000373414" "ENSP00000362513" "P35504" "UGT1A5" "54579" "UDP glucuronosyltransferase family 1 member A5" "UGT1E" "Endoplasmic reticulum" "SwissProt" +"ENSG00000007314" "" "" "" "" "" "" "" "" "" +"ENSG00000102452" "" "" "" "" "" "" "" "" "" +"ENSG00000136531" "" "" "" "" "" "" "" "" "" +"ENSG00000136546" "" "" "" "" "" "" "" "" "" +"ENSG00000138622" "" "" "" "" "" "" "" "" "" +"ENSG00000144285" "" "" "" "" "" "" "" "" "" +"ENSG00000162341" "" "" "" "" "" "" "" "" "" +"ENSG00000164588" "" "" "" "" "" "" "" "" "" +"ENSG00000168356" "" "" "" "" "" "" "" "" "" +"ENSG00000169432" "" "" "" "" "" "" "" "" "" +"ENSG00000183873" "" "" "" "" "" "" "" "" "" +"ENSG00000185313" "" "" "" "" "" "" "" "" "" +"ENSG00000186815" "" "" "" "" "" "" "" "" "" +"ENSG00000196876" "" "" "" "" "" "" "" "" "" From eb4d76d4d29feaf9d047f1b2b17a51bba7a109d8 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 21 Jun 2023 15:17:16 -0400 Subject: [PATCH 3/9] fix: added info for new genes to genes.tsv --- model/genes.tsv | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/model/genes.tsv b/model/genes.tsv index 6cd89bd0..d0261d0c 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2896,17 +2896,17 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000281500" "ENST00000525102;ENST00000330775;ENST00000357590;ENST00000538950;ENST00000545985;ENST00000526275;ENST00000532085;ENST00000650539;ENST00000527992;ENST00000638925;ENST00000638360;ENST00000638186;ENST00000530407;ENST00000524428;ENST00000525372;ENST00000525039;ENST00000529510;ENST00000532888;ENST00000526626;ENST00000525787;ENST00000534384" "ENSP00000476242;ENSP00000476176;ENSP00000475991;ENSP00000475241" "O43826" "SLC37A4" "" "Glucose-6-phosphate exchanger" "G6PT,G6PT1" "Endoplasmic reticulum" "SwissProt" "ENSG00000288702" "ENST00000482026" "ENSP00000418532" "P35503" "UGT1A3" "54659" "UDP glucuronosyltransferase family 1 member A3" "UGT1C" "Endoplasmic reticulum" "SwissProt" "ENSG00000288705" "ENST00000373414" "ENSP00000362513" "P35504" "UGT1A5" "54579" "UDP glucuronosyltransferase family 1 member A5" "UGT1E" "Endoplasmic reticulum" "SwissProt" -"ENSG00000007314" "" "" "" "" "" "" "" "" "" -"ENSG00000102452" "" "" "" "" "" "" "" "" "" -"ENSG00000136531" "" "" "" "" "" "" "" "" "" -"ENSG00000136546" "" "" "" "" "" "" "" "" "" -"ENSG00000138622" "" "" "" "" "" "" "" "" "" -"ENSG00000144285" "" "" "" "" "" "" "" "" "" -"ENSG00000162341" "" "" "" "" "" "" "" "" "" -"ENSG00000164588" "" "" "" "" "" "" "" "" "" -"ENSG00000168356" "" "" "" "" "" "" "" "" "" -"ENSG00000169432" "" "" "" "" "" "" "" "" "" -"ENSG00000183873" "" "" "" "" "" "" "" "" "" -"ENSG00000185313" "" "" "" "" "" "" "" "" "" -"ENSG00000186815" "" "" "" "" "" "" "" "" "" -"ENSG00000196876" "" "" "" "" "" "" "" "" "" +"ENSG00000007314" "ENST00000435607" "ENSP00000396320" "P35499" "SCN4A" "6329" "sodium voltage-gated channel alpha subunit 4" "" "" "" +"ENSG00000102452" "ENST00000675594;ENST00000497170;ENST00000675802;ENST00000251127;ENST00000376200;ENST00000467264;ENST00000676315;ENST00000648359;ENST00000675150;ENST00000675332" "ENSP00000502675;ENSP00000501603;ENSP00000365373;ENSP00000501955;ENSP00000502680;ENSP00000497465;ENSP00000501818;ENSP00000502490;ENSP00000251127;ENSP00000502148" "Q8IZF0" "NALCN" "259232" "sodium leak channel, non-selective" "" "" "" +"ENSG00000136531" "ENST00000636769;ENST00000637367;ENST00000673831;ENST00000674133;ENST00000486878;ENST00000636071;ENST00000631182;ENST00000424833;ENST00000673883;ENST00000636135;ENST00000636384;ENST00000636662;ENST00000283256;ENST00000375437;ENST00000637266;ENST00000636985" "ENSP00000406454;ENSP00000490592;ENSP00000364586;ENSP00000490765;ENSP00000490107;ENSP00000501305;ENSP00000490849;ENSP00000501309;ENSP00000486885;ENSP00000489873;ENSP00000489821;ENSP00000283256;ENSP00000487466;ENSP00000490800;ENSP00000500975;ENSP00000490866" "Q99250" "SCN2A" "6326" "sodium voltage-gated channel alpha subunit 2" "" "" "" +"ENSG00000136546" "ENST00000650747;ENST00000643258;ENST00000419992;ENST00000424326;ENST00000441411" "ENSP00000496114;ENSP00000498959;ENSP00000413699;ENSP00000403846;ENSP00000396600" "Q01118" "SCN7A" "6332" "sodium voltage-gated channel alpha subunit 7" "" "" "" +"ENSG00000138622" "ENST00000261917" "ENSP00000261917" "Q9Y3Q4" "HCN4" "10021" "hyperpolarization activated cyclic nucleotide gated potassium channel 4" "" "" "" +"ENSG00000144285" "ENST00000689288;ENST00000409050;ENST00000674923;ENST00000636759;ENST00000641603;ENST00000641996;ENST00000637988;ENST00000637285;ENST00000641575;ENST00000671940;ENST00000635750;ENST00000375405;ENST00000636194;ENST00000303395;ENST00000637038;ENST00000635776;ENST00000640036" "ENSP00000490612;ENSP00000490780;ENSP00000490895;ENSP00000492917;ENSP00000500336;ENSP00000303540;ENSP00000509637;ENSP00000490799;ENSP00000364554;ENSP00000493054;ENSP00000490692;ENSP00000492945;ENSP00000490288;ENSP00000501589;ENSP00000386312;ENSP00000491573;ENSP00000490184" "P35498" "SCN1A" "6323" "sodium voltage-gated channel alpha subunit 1" "" "" "" +"ENSG00000162341" "ENST00000637342;ENST00000635811;ENST00000294309;ENST00000637504;ENST00000542467" "ENSP00000490341;ENSP00000294309;ENSP00000445551;ENSP00000490171;ENSP00000489759" "Q8NHX9" "TPCN2" "219931" "two pore segment channel 2" "" "" "" +"ENSG00000164588" "ENST00000634658;ENST00000673735;ENST00000303230" "ENSP00000489134;ENSP00000501107;ENSP00000307342" "O60741" "HCN1" "348980" "hyperpolarization activated cyclic nucleotide gated potassium channel 1" "" "" "" +"ENSG00000168356" "ENST00000675892;ENST00000675223;ENST00000444237;ENST00000676045;ENST00000456224;ENST00000676176;ENST00000675672;ENST00000668754;ENST00000302328" "ENSP00000502318;ENSP00000499569;ENSP00000408028;ENSP00000502481;ENSP00000502446;ENSP00000307599;ENSP00000416757;ENSP00000501891;ENSP00000501685" "Q9UI33" "SCN11A" "11280" "sodium voltage-gated channel alpha subunit 11" "" "" "" +"ENSG00000169432" "ENST00000645907;ENST00000452182;ENST00000303354;ENST00000643319;ENST00000645283;ENST00000642356;ENST00000667991;ENST00000667201;ENST00000454569;ENST00000409672" "ENSP00000386306;ENSP00000495983;ENSP00000413212;ENSP00000496086;ENSP00000499663;ENSP00000304748;ENSP00000393141;ENSP00000499341;ENSP00000494071;ENSP00000495601" "Q15858" "SCN9A" "6335" "sodium voltage-gated channel alpha subunit 9" "" "" "" +"ENSG00000183873" "ENST00000333535;ENST00000413689;ENST00000414099;ENST00000450102;ENST00000449557;ENST00000455624;ENST00000423572;ENST00000327956" "ENSP00000398266;ENSP00000413996;ENSP00000410257;ENSP00000399524;ENSP00000398962;ENSP00000333674;ENSP00000328968;ENSP00000403355" "Q14524" "SCN5A" "6331" "sodium voltage-gated channel alpha subunit 5" "" "" "" +"ENSG00000185313" "ENST00000655275;ENST00000449082;ENST00000643924" "ENSP00000499510;ENSP00000495595;ENSP00000390600" "Q9Y5Y9" "SCN10A" "6336" "sodium voltage-gated channel alpha subunit 10" "" "" "" +"ENSG00000186815" "ENST00000335509;ENST00000551099;ENST00000552642;ENST00000392569;ENST00000552985;ENST00000552542;ENST00000547955;ENST00000547275;ENST00000548465;ENST00000546781;ENST00000550873;ENST00000551096;ENST00000549279;ENST00000541517;ENST00000550785;ENST00000552897" "ENSP00000448010;ENSP00000448561;ENSP00000449560;ENSP00000447569;ENSP00000438125;ENSP00000335300;ENSP00000446767;ENSP00000448083;ENSP00000447181;ENSP00000447806;ENSP00000447263;ENSP00000448704;ENSP00000447073;ENSP00000449944;ENSP00000449564;ENSP00000376350" "Q9ULQ1" "TPCN1" "53373" "two pore segment channel 1" "" "" "" +"ENSG00000196876" "ENST00000662684;ENST00000627620;ENST00000599343;ENST00000548086;ENST00000551216;ENST00000355133;ENST00000667214;ENST00000546961;ENST00000545061;ENST00000638820;ENST00000354534;ENST00000637709;ENST00000636945;ENST00000668547" "ENSP00000447567;ENSP00000499511;ENSP00000490470;ENSP00000492157;ENSP00000499724;ENSP00000486828;ENSP00000347255;ENSP00000476447;ENSP00000346534;ENSP00000487583;ENSP00000490580;ENSP00000440360;ENSP00000499691;ENSP00000499636" "Q9UQD0" "SCN8A" "6334" "sodium voltage-gated channel alpha subunit 8" "" "" "" From 8cb8f7848db7d706124b70cf2f8b9782e9f3fc2f Mon Sep 17 00:00:00 2001 From: Mihail Anton Date: Tue, 11 Jul 2023 05:07:28 +1200 Subject: [PATCH 4/9] refactor: improve test output in test workflow --- code/test/sanityCheck.py | 22 ++++++++++++++++------ 1 file changed, 16 insertions(+), 6 deletions(-) diff --git a/code/test/sanityCheck.py b/code/test/sanityCheck.py index f1afed80..12e8d035 100644 --- a/code/test/sanityCheck.py +++ b/code/test/sanityCheck.py @@ -38,8 +38,12 @@ def checkRxnAnnotation(rxns): rxnList = get_column_from_tsv("model/reactions.tsv", "rxns") spontaneous = get_column_from_tsv("model/reactions.tsv", "spontaneous", False) rxnDeprecated = get_column_from_tsv("data/deprecatedIdentifiers/deprecatedReactions.tsv", "rxns") - assert set(rxnList).isdisjoint(set(rxnDeprecated)), "Deprecated reaction reused!" - assert rxnList == rxns, "Reaction annotation mismatch!" + rxnMisused = set(rxns).intersection(set(rxnDeprecated)) + assert len(rxnMisused) == 0, "Deprecated reaction(s) used: {}".format(rxnMisused) + rxnMisused = set(rxns).difference(set(rxnList)) + assert len(rxnMisused) == 0, "Reaction(s) not annotated in reactions.tsv: {}".format(rxnMisused) + rxnMisused = set(rxnList).difference(set(rxns)) + assert len(rxnMisused) == 0, "Annotated reactions are missing from the model: {}".format(rxnMisused) assert pd.api.types.is_numeric_dtype(spontaneous), "Spontaneous column should be in numeric!" @@ -49,16 +53,22 @@ def checkMetAnnotation(mets): """ metList = get_column_from_tsv("model/metabolites.tsv", "mets") metDeprecated = get_column_from_tsv("data/deprecatedIdentifiers/deprecatedMetabolites.tsv", "mets") - assert set(metList).isdisjoint(set(metDeprecated)), "Deprecated metabolite reused!" - assert metList == mets, "Metabolite annotation mismatch!" - + metMisused = set(mets).intersection(set(metDeprecated)) + assert len(metMisused) == 0, "Deprecated metabolite(s) used: {}".format(metMisused) + metMisused = set(mets).difference(set(metList)) + assert len(metMisused) == 0, "Metabolite(s) not annotated in metabolites.tsv: {}".format(metMisused) + metMisused = set(metList).difference(set(mets)) + assert len(metMisused) == 0, "Annotated metabolite(s) are missing from the model: {}".format(metMisused) def checkGeneAnnotation(genes): """ check consistency of gene lists between model and annotation file """ geneList = get_column_from_tsv("model/genes.tsv", "genes") - assert geneList == genes, "Gene annotation mismatch!" + geneMisused = set(genes).difference(set(geneList)) + assert len(geneMisused) == 0, "Gene(s) not annotated in genes.tsv: {}".format(geneMisused) + geneMisused = set(geneList).difference(set(genes)) + assert len(geneMisused) == 0, "Annotated gene(s) are missing from the model: {}".format(geneMisused) def find_unused_entities(model, entity_type): From ad5726c0b999a5da1d27f50de63da323fe34d4df Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Tue, 1 Aug 2023 14:31:58 -0400 Subject: [PATCH 5/9] fix: added in some genes I missed the first time --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 935caea1..dbe3fffc 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -225083,7 +225083,7 @@ - MAM02519e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000007314 or ENSG00000102452 or ENSG00000136531 or ENSG00000136546 or ENSG00000138622 or ENSG00000144285 or ENSG00000162341 or ENSG00000164588 or ENSG00000168356 or ENSG00000169432 or ENSG00000183873 or ENSG00000185313 or ENSG00000186815 or ENSG00000196876" + - gene_reaction_rule: "ENSG00000144285 or ENSG00000136531 or ENSG00000153253 or ENSG00000007314 or ENSG00000183873 or ENSG00000136546 or ENSG00000196876 or ENSG00000169432 or ENSG00000185313 or ENSG00000168356 or ENSG00000111319 or ENSG00000168447 or ENSG00000162572 or ENSG00000166828 or ENSG00000164588 or ENSG00000138622 or ENSG00000186815 or ENSG00000162341 or ENSG00000102452" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" From 3acaae05f0f7bb2d5caa13b04b5d4c59a9fee13a Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Tue, 1 Aug 2023 14:36:54 -0400 Subject: [PATCH 6/9] fix: add new gene entries for new genes --- model/Human-GEM.yml | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index dbe3fffc..fc9c2c85 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -307464,6 +307464,9 @@ - !!omap - id: "ENSG00000111275" - name: "ALDH2" + - !!omap + - id: "ENSG00000111319" + - name: "SCNN1A" - !!omap - id: "ENSG00000111339" - name: "ART4" @@ -310344,6 +310347,9 @@ - !!omap - id: "ENSG00000153207" - name: "AHCTF1" + - !!omap + - id: "ENSG00000153253" + - name: "SCN3A" - !!omap - id: "ENSG00000153291" - name: "SLC25A27" @@ -310902,6 +310908,9 @@ - !!omap - id: "ENSG00000162551" - name: "ALPL" + - !!omap + - id: "ENSG00000162572" + - name: "SCNN1D" - !!omap - id: "ENSG00000162607" - name: "USP1" @@ -311397,6 +311406,9 @@ - !!omap - id: "ENSG00000166825" - name: "ANPEP" + - !!omap + - id: "ENSG00000166828" + - name: "SCNN1G" - !!omap - id: "ENSG00000166840" - name: "GLYATL1" @@ -311604,6 +311616,9 @@ - !!omap - id: "ENSG00000168411" - name: "RFWD3" + - !!omap + - id: "ENSG00000168447" + - name: "SCNN1B" - !!omap - id: "ENSG00000168487" - name: "BMP1" From 25251aa2d08f9f0e1f237b42e58f700583c70f68 Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Tue, 1 Aug 2023 15:12:47 -0400 Subject: [PATCH 7/9] fix: update model/genes.tsv --- model/genes.tsv | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/model/genes.tsv b/model/genes.tsv index fa3fba65..4b17c98d 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -2879,3 +2879,8 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen "ENSG00000185313" "ENST00000655275;ENST00000449082;ENST00000643924" "ENSP00000499510;ENSP00000495595;ENSP00000390600" "Q9Y5Y9" "SCN10A" "6336" "sodium voltage-gated channel alpha subunit 10" "" "" "" "ENSG00000186815" "ENST00000335509;ENST00000551099;ENST00000552642;ENST00000392569;ENST00000552985;ENST00000552542;ENST00000547955;ENST00000547275;ENST00000548465;ENST00000546781;ENST00000550873;ENST00000551096;ENST00000549279;ENST00000541517;ENST00000550785;ENST00000552897" "ENSP00000448010;ENSP00000448561;ENSP00000449560;ENSP00000447569;ENSP00000438125;ENSP00000335300;ENSP00000446767;ENSP00000448083;ENSP00000447181;ENSP00000447806;ENSP00000447263;ENSP00000448704;ENSP00000447073;ENSP00000449944;ENSP00000449564;ENSP00000376350" "Q9ULQ1" "TPCN1" "53373" "two pore segment channel 1" "" "" "" "ENSG00000196876" "ENST00000662684;ENST00000627620;ENST00000599343;ENST00000548086;ENST00000551216;ENST00000355133;ENST00000667214;ENST00000546961;ENST00000545061;ENST00000638820;ENST00000354534;ENST00000637709;ENST00000636945;ENST00000668547" "ENSP00000447567;ENSP00000499511;ENSP00000490470;ENSP00000492157;ENSP00000499724;ENSP00000486828;ENSP00000347255;ENSP00000476447;ENSP00000346534;ENSP00000487583;ENSP00000490580;ENSP00000440360;ENSP00000499691;ENSP00000499636" "Q9UQD0" "SCN8A" "6334" "sodium voltage-gated channel alpha subunit 8" "" "" "" +"ENSG00000166828" "ENST00000300061" "ENSP00000300061" "P51170" "SCNN1G" "6340" "sodium channel epithelial 1 subunit gamma" "" "" "" +"ENSG00000168447" "ENST00000343070;ENST00000307331;ENST00000568923;ENST00000568085;ENST00000566441" "ENSP00000345751;ENSP00000302874;ENSP00000456309;ENSP00000455673;ENSP00000482681" "P51168" "SCNN1B" "6338" "sodium channel epithelial 1 subunit beta" "" "" "" +"ENSG00000111319" "ENST00000228916;ENST00000360168;ENST00000540037;ENST00000543768;ENST00000396966;ENST00000536788" "ENSP00000228916;ENSP00000353292;ENSP00000440876;ENSP00000438739;ENSP00000380166;ENSP00000443434" "P37088" "SCNN1A" "6337" "sodium channel epithelial 1 subunit alpha" "" "" "" +"ENSG00000162572" "ENST00000379116;ENST00000338555;ENST00000400928;ENST00000325425;ENST00000379099;ENST00000470022" "ENSP00000368411;ENSP00000339504;ENSP00000383717;ENSP00000321594;ENSP00000368393;ENSP00000420548" "P51172" "SCNN1D" "6339" "sodium channel epithelial 1 subunit delta" "" "" "" +"ENSG00000153253" "ENST00000283254;ENST00000706067;ENST00000639244;ENST00000409101;ENST00000668657;ENST00000440431;ENST00000453007" "ENSP00000283254;ENSP00000516211;ENSP00000492251;ENSP00000386726;ENSP00000499420;ENSP00000403348;ENSP00000391569" "Q9NY46" "SCN3A" "6328" "sodium voltage-gated channel alpha subunit 3" "" "" "" From 6b696d3b18ac06d888ddb1e5a58ceb7a71da129c Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 2 Aug 2023 08:46:45 -0400 Subject: [PATCH 8/9] fix: AND together SCNN1A, SCNN1B, and SCNN1G since they form a trimer --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index fc9c2c85..99c23dd0 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -225083,7 +225083,7 @@ - MAM02519e: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000144285 or ENSG00000136531 or ENSG00000153253 or ENSG00000007314 or ENSG00000183873 or ENSG00000136546 or ENSG00000196876 or ENSG00000169432 or ENSG00000185313 or ENSG00000168356 or ENSG00000111319 or ENSG00000168447 or ENSG00000162572 or ENSG00000166828 or ENSG00000164588 or ENSG00000138622 or ENSG00000186815 or ENSG00000162341 or ENSG00000102452" + - gene_reaction_rule: "ENSG00000144285 or ENSG00000136531 or ENSG00000153253 or ENSG00000007314 or ENSG00000183873 or ENSG00000136546 or ENSG00000196876 or ENSG00000169432 or ENSG00000185313 or ENSG00000168356 or ENSG00000164588 or ENSG00000138622 or ENSG00000186815 or ENSG00000162341 or ENSG00000102452 or (ENSG00000111319 and ENSG00000168447 and ENSG00000166828) or ENSG00000162572" - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" From 1d868a6e189259fdec18967f9a83fae11857f33f Mon Sep 17 00:00:00 2001 From: Devlin-Moyer Date: Wed, 2 Aug 2023 08:50:53 -0400 Subject: [PATCH 9/9] feat: added refs for SCNN1A/B/G/D complex/isozyme situation --- model/Human-GEM.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 99c23dd0..c2f410e0 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -225087,7 +225087,7 @@ - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "" - - references: "PMID:10893432;PMID:11024018;PMID:11034615;PMID:12679487;PMID:12748858;PMID:1372904;PMID:15546855;PMID:2490366;PMID:7537337;PMID:7789985;PMID:8063771;PMID:8559252;PMID:8806637;PMID:9341168" + - references: "PMID:10893432;PMID:11024018;PMID:11034615;PMID:12679487;PMID:12748858;PMID:1372904;PMID:15546855;PMID:2490366;PMID:7537337;PMID:7789985;PMID:8063771;PMID:8559252;PMID:8806637;PMID:9341168;PMID:22573384;PMID:26772908" - subsystem: - "Transport reactions" - confidence_score: 0