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Merge pull request #664 from SysBioChalmers/fix/sodium_channel_genes
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add Alpha subunits of sodium channel genes to MAR01527
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@haowang-bioinfo
haowang-bioinfo authored Aug 3, 2023
2 parents 5896d8c + 1d868a6 commit 0745ddf
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Showing 3 changed files with 94 additions and 8 deletions.
22 changes: 16 additions & 6 deletions code/test/sanityCheck.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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!"


Expand All @@ -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):
Expand Down
61 changes: 59 additions & 2 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -225083,11 +225083,11 @@
- MAM02519e: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000100170 or ENSG00000105641 or ENSG00000198743"
- 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: ""
- 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
Expand Down Expand Up @@ -305364,6 +305364,9 @@
- !!omap
- id: "ENSG00000007216"
- name: "SLC13A2"
- !!omap
- id: "ENSG00000007314"
- name: "SCN4A"
- !!omap
- id: "ENSG00000007350"
- name: "TKTL1"
Expand Down Expand Up @@ -306819,6 +306822,9 @@
- !!omap
- id: "ENSG00000102393"
- name: "GLA"
- !!omap
- id: "ENSG00000102452"
- name: "NALCN"
- !!omap
- id: "ENSG00000102575"
- name: "ACP5"
Expand Down Expand Up @@ -307458,6 +307464,9 @@
- !!omap
- id: "ENSG00000111275"
- name: "ALDH2"
- !!omap
- id: "ENSG00000111319"
- name: "SCNN1A"
- !!omap
- id: "ENSG00000111339"
- name: "ART4"
Expand Down Expand Up @@ -309132,12 +309141,18 @@
- !!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"
Expand Down Expand Up @@ -309348,6 +309363,9 @@
- !!omap
- id: "ENSG00000138621"
- name: "PPCDC"
- !!omap
- id: "ENSG00000138622"
- name: "HCN4"
- !!omap
- id: "ENSG00000138641"
- name: "HERC3"
Expand Down Expand Up @@ -309840,6 +309858,9 @@
- !!omap
- id: "ENSG00000144278"
- name: "GALNT13"
- !!omap
- id: "ENSG00000144285"
- name: "SCN1A"
- !!omap
- id: "ENSG00000144290"
- name: "SLC4A10"
Expand Down Expand Up @@ -310326,6 +310347,9 @@
- !!omap
- id: "ENSG00000153207"
- name: "AHCTF1"
- !!omap
- id: "ENSG00000153253"
- name: "SCN3A"
- !!omap
- id: "ENSG00000153291"
- name: "SLC25A27"
Expand Down Expand Up @@ -310848,6 +310872,9 @@
- !!omap
- id: "ENSG00000162298"
- name: "SYVN1"
- !!omap
- id: "ENSG00000162341"
- name: "TPCN2"
- !!omap
- id: "ENSG00000162365"
- name: "CYP4A22"
Expand Down Expand Up @@ -310881,6 +310908,9 @@
- !!omap
- id: "ENSG00000162551"
- name: "ALPL"
- !!omap
- id: "ENSG00000162572"
- name: "SCNN1D"
- !!omap
- id: "ENSG00000162607"
- name: "USP1"
Expand Down Expand Up @@ -311127,6 +311157,9 @@
- !!omap
- id: "ENSG00000164574"
- name: "GALNT10"
- !!omap
- id: "ENSG00000164588"
- name: "HCN1"
- !!omap
- id: "ENSG00000164638"
- name: "SLC29A4"
Expand Down Expand Up @@ -311373,6 +311406,9 @@
- !!omap
- id: "ENSG00000166825"
- name: "ANPEP"
- !!omap
- id: "ENSG00000166828"
- name: "SCNN1G"
- !!omap
- id: "ENSG00000166840"
- name: "GLYATL1"
Expand Down Expand Up @@ -311571,12 +311607,18 @@
- !!omap
- id: "ENSG00000168350"
- name: "DEGS2"
- !!omap
- id: "ENSG00000168356"
- name: "SCN11A"
- !!omap
- id: "ENSG00000168393"
- name: "DTYMK"
- !!omap
- id: "ENSG00000168411"
- name: "RFWD3"
- !!omap
- id: "ENSG00000168447"
- name: "SCNN1B"
- !!omap
- id: "ENSG00000168487"
- name: "BMP1"
Expand Down Expand Up @@ -311658,6 +311700,9 @@
- !!omap
- id: "ENSG00000169418"
- name: "NPR1"
- !!omap
- id: "ENSG00000169432"
- name: "SCN9A"
- !!omap
- id: "ENSG00000169660"
- name: "HEXD"
Expand Down Expand Up @@ -312621,6 +312666,9 @@
- !!omap
- id: "ENSG00000183828"
- name: "NUDT14"
- !!omap
- id: "ENSG00000183873"
- name: "SCN5A"
- !!omap
- id: "ENSG00000183921"
- name: "SDR42E2"
Expand Down Expand Up @@ -312714,6 +312762,9 @@
- !!omap
- id: "ENSG00000185274"
- name: "GALNT17"
- !!omap
- id: "ENSG00000185313"
- name: "SCN10A"
- !!omap
- id: "ENSG00000185344"
- name: "ATP6V0A2"
Expand Down Expand Up @@ -312825,6 +312876,9 @@
- !!omap
- id: "ENSG00000186792"
- name: "HYAL3"
- !!omap
- id: "ENSG00000186815"
- name: "TPCN1"
- !!omap
- id: "ENSG00000186908"
- name: "ZDHHC17"
Expand Down Expand Up @@ -313002,6 +313056,9 @@
- !!omap
- id: "ENSG00000196839"
- name: "ADA"
- !!omap
- id: "ENSG00000196876"
- name: "SCN8A"
- !!omap
- id: "ENSG00000196950"
- name: "SLC39A10"
Expand Down
19 changes: 19 additions & 0 deletions model/genes.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -2865,3 +2865,22 @@ 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" "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" "" "" ""
"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" "" "" ""

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