Merge pull request #965 from SysBioChalmers/Fix-remove_nonassociated_…

…genes Fix: remove nonassociated genes
SysBioChalmers · Feb 12, 2025 · 1aa9597 · 1aa9597
2 parents 2e73454 + 0fd1c6e
commit 1aa9597
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diff --git a/data/testResults/README.md b/data/testResults/README.md
@@ -4,8 +4,8 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/
 
 The test results shown here were obtained by the GitHub Actions run in:
 
-- **PR #951** (MACAW)
-- **PR #951** (gene essentiality)
+- **PR #965** (MACAW)
+- **PR #965** (gene essentiality)
 
 The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request.
 

diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv
@@ -1,7 +1,7 @@
 cellLine,TP,TN,FP,FN,accuracy,sensitivity,specificity,F1,MCC
-DLD1,50,2145,85,272,0.8601,0.1553,0.9619,0.2188,0.1738
-GBM,57,2136,78,280,0.8597,0.1691,0.9648,0.2415,0.2025
-HCT116,71,2178,70,288,0.8627,0.1978,0.9689,0.284,0.2539
-HELA,35,2218,106,250,0.8635,0.1228,0.9544,0.1643,0.1065
-RPE1,21,2161,114,255,0.8554,0.07609,0.9499,0.1022,0.03604
-all,8,2355,133,113,0.9057,0.06612,0.9465,0.06107,0.01177
+DLD1,50,2134,84,268,0.8612,0.1572,0.9621,0.2212,0.1767
+GBM,57,2124,77,277,0.8604,0.1707,0.965,0.2436,0.2051
+HCT116,71,2167,69,284,0.8638,0.2,0.9691,0.2869,0.2573
+HELA,35,2206,105,247,0.8642,0.1241,0.9546,0.1659,0.1084
+RPE1,21,2149,113,252,0.856,0.07692,0.95,0.1032,0.03736
+all,8,2342,132,111,0.9063,0.06723,0.9466,0.06178,0.01284
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -119719,7 +119719,7 @@
           - MAM10007c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000087253 or ENSG00000111684 or ENSG00000153395 or ENSG00000176454"
+      - gene_reaction_rule: "ENSG00000087253 or ENSG00000111684 or ENSG00000123684 or ENSG00000153395 or ENSG00000176454"
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.3.1.23"
       - subsystem:
@@ -150993,7 +150993,7 @@
           - MAM01619e: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000130821"
+      - gene_reaction_rule: "ENSG00000130821 or ENSG00000165449"
       - rxnFrom: "HMRdatabase"
       - references: "PMID:11165387;PMID:12110547;PMID:12145274;PMID:15918910;PMID:3896131;PMID:9386672"
       - subsystem:
@@ -261836,9 +261836,6 @@
     - !!omap
       - id: "ENSG00000102575"
       - name: "ACP5"
-    - !!omap
-      - id: "ENSG00000102595"
-      - name: "UGGT2"
     - !!omap
       - id: "ENSG00000102699"
       - name: "PARP4"
@@ -264167,9 +264164,6 @@
     - !!omap
       - id: "ENSG00000136720"
       - name: "HS6ST1"
-    - !!omap
-      - id: "ENSG00000136731"
-      - name: "UGGT1"
     - !!omap
       - id: "ENSG00000136750"
       - name: "GAD2"
@@ -265010,9 +265004,6 @@
     - !!omap
       - id: "ENSG00000147160"
       - name: "AWAT2"
-    - !!omap
-      - id: "ENSG00000147162"
-      - name: "OGT"
     - !!omap
       - id: "ENSG00000147224"
       - name: "PRPS1"
@@ -267215,9 +267206,6 @@
     - !!omap
       - id: "ENSG00000175567"
       - name: "UCP2"
-    - !!omap
-      - id: "ENSG00000175711"
-      - name: "B3GNTL1"
     - !!omap
       - id: "ENSG00000175806"
       - name: "MSRA"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -522,7 +522,6 @@
 "ENSG00000102383"	"ENST00000373367;ENST00000482827;ENST00000541184"	"ENSP00000362465;ENSP00000445420"	"Q96MV8"	"ZDHHC15"	"158866"	"zinc finger DHHC-type palmitoyltransferase 15"	"DHHC15;FLJ31812;MRX91"	"Golgi apparatus;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000102393"	"ENST00000674142;ENST00000468823;ENST00000493905;ENST00000218516;ENST00000466414;ENST00000479445;ENST00000649178;ENST00000675968;ENST00000676156;ENST00000675592;ENST00000676372;ENST00000674127;ENST00000675799;ENST00000486121;ENST00000480513;ENST00000674634"	"ENSP00000476935;ENSP00000218516;ENSP00000498186;ENSP00000501730;ENSP00000502239;ENSP00000502805;ENSP00000501044;ENSP00000502661;ENSP00000501124;ENSP00000497055;ENSP00000502629"	"P06280"	"GLA"	"2717"	"galactosidase alpha"	"GALA"	"Lysosome"	"SwissProt"
 "ENSG00000102575"	"ENST00000648477;ENST00000218758;ENST00000412435;ENST00000590420;ENST00000588625;ENST00000588524;ENST00000590832;ENST00000588079;ENST00000589792;ENST00000649386;ENST00000591319;ENST00000592828;ENST00000592659"	"ENSP00000496973;ENSP00000218758;ENSP00000392374;ENSP00000468509;ENSP00000465127;ENSP00000468685;ENSP00000497140;ENSP00000464831;ENSP00000468767;ENSP00000465498"	"P13686"	"ACP5"	"54"	"acid phosphatase 5, tartrate resistant"	"HPAP;TRAP"	"Cytosol;Lysosome"	"SwissProt;CellAtlas"
-"ENSG00000102595"	"ENST00000376747;ENST00000462472;ENST00000476866;ENST00000491509;ENST00000463054;ENST00000465196;ENST00000461329;ENST00000467305;ENST00000376712;ENST00000376714;ENST00000621375;ENST00000397618;ENST00000638479"	"ENSP00000365938;ENSP00000365902;ENSP00000365904;ENSP00000482021;ENSP00000380743;ENSP00000491729"	"Q9NYU1"	"UGGT2"	"55757"	"UDP-glucose glycoprotein glucosyltransferase 2"	"FLJ10873;FLJ11485;HUGT2;MGC117360;MGC150689;MGC87276;UGCGL2"	"Endoplasmic reticulum"	"SwissProt"
 "ENSG00000102699"	"ENST00000381989;ENST00000484989;ENST00000480576"	"ENSP00000371419"	"Q9UKK3"	"PARP4"	"143"	"poly(ADP-ribose) polymerase family member 4"	"ADPRTL1;ARTD4;p193;VAULT3;VPARP;VWA5C"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000102743"	"ENST00000478827;ENST00000338625;ENST00000417731;ENST00000470509"	"ENSP00000342267;ENSP00000415826;ENSP00000431429"	"Q9Y619"	"SLC25A15"	"10166"	"solute carrier family 25 member 15"	"D13S327;HHH;ORC1;ORNT1"	"Inner mitochondria"	"SwissProt"
 "ENSG00000102780"	"ENST00000337343;ENST00000261491;ENST00000611224;ENST00000628433;ENST00000627777;ENST00000626247;ENST00000536612;ENST00000498255;ENST00000489851;ENST00000379274"	"ENSP00000337572;ENSP00000261491;ENSP00000482250;ENSP00000485809;ENSP00000486838;ENSP00000486329;ENSP00000445114;ENSP00000368576"	"Q86XP1"	"DGKH"	"160851"	"diacylglycerol kinase eta"	"DGKeta"	"Cytosol"	"SwissProt"
@@ -1290,7 +1289,6 @@
 "ENSG00000136628"	"ENST00000366923;ENST00000468487;ENST00000485821;ENST00000609181;ENST00000464052;ENST00000477030"	"ENSP00000355890;ENSP00000477245;ENSP00000477493"	"P07814"	"EPRS1"	"2058"	"glutamyl-prolyl-tRNA synthetase 1"	"EARS;EPRS;GLUPRORS;PARS;QARS;QPRS"	"Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000136699"	"ENST00000431183;ENST00000454468;ENST00000412570;ENST00000433118;ENST00000351288;ENST00000680298;ENST00000491128;ENST00000482171;ENST00000439886;ENST00000409031;ENST00000680401;ENST00000680679;ENST00000680810;ENST00000680987;ENST00000457039;ENST00000491319;ENST00000449159;ENST00000461187;ENST00000430682;ENST00000451542;ENST00000435455;ENST00000680196;ENST00000473720;ENST00000455548;ENST00000439029;ENST00000681660;ENST00000441135"	"ENSP00000405187;ENSP00000407591;ENSP00000403002;ENSP00000397278;ENSP00000259217;ENSP00000506463;ENSP00000401648;ENSP00000386531;ENSP00000506367;ENSP00000505716;ENSP00000505271;ENSP00000506346;ENSP00000397078;ENSP00000403915;ENSP00000406325;ENSP00000405363;ENSP00000393791;ENSP00000505151;ENSP00000416208;ENSP00000406458"	"Q9NXE4"	"SMPD4"	"55627"	"sphingomyelin phosphodiesterase 4"	"FLJ20297;FLJ20756;KIAA1418;NET13;nSMase-3;NSMASE3"	"Endoplasmic reticulum;Golgi apparatus;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000136720"	"ENST00000469019;ENST00000259241;ENST00000463963;ENST00000494089"	"ENSP00000259241"	"O60243"	"HS6ST1"	"9394"	"heparan sulfate 6-O-sulfotransferase 1"	"HS6ST"	"Nucleus"	"CellAtlas"
-"ENSG00000136731"	"ENST00000430075;ENST00000438277;ENST00000376723;ENST00000259253;ENST00000488439;ENST00000418197;ENST00000465836"	"ENSP00000400426;ENSP00000392701;ENSP00000365913;ENSP00000259253;ENSP00000389441"	"Q9NYU2"	"UGGT1"	"56886"	"UDP-glucose glycoprotein glucosyltransferase 1"	"HUGT1;UGCGL1"	"Endoplasmic reticulum;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000136750"	"ENST00000376261;ENST00000259271;ENST00000428517;ENST00000648567;ENST00000376248"	"ENSP00000365437;ENSP00000259271;ENSP00000390434;ENSP00000498009"	"Q05329"	"GAD2"	"2572"	"glutamate decarboxylase 2"	"GAD65"	"Cytosol;Golgi apparatus"	"SwissProt"
 "ENSG00000136810"	"ENST00000374515;ENST00000374517;ENST00000487892"	"ENSP00000363639;ENSP00000363641"	"P10599"	"TXN"	"7295"	"thioredoxin"	"TRX"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000136840"	"ENST00000335791;ENST00000495983;ENST00000474282;ENST00000467674;ENST00000361444;ENST00000483438;ENST00000479747"	"ENSP00000336733;ENSP00000355130"	"Q9H4F1"	"ST6GALNAC4"	"27090"	"ST6 N-acetylgalactosaminide alpha-2,6-sialyltransferase 4"	"SIAT3C;SIAT7D;ST6GALNACIV"	"Golgi apparatus;Nucleus"	"CellAtlas"
@@ -1567,7 +1565,6 @@
 "ENSG00000147123"	"ENST00000377811;ENST00000276062"	"ENSP00000367042;ENSP00000276062"	"Q9NX14"	"NDUFB11"	"54539"	"NADH:ubiquinone oxidoreductase subunit B11"	"ESSS;Np15;NP17.3"	"Inner mitochondria"	"SwissProt;CellAtlas"
 "ENSG00000147155"	"ENST00000276096;ENST00000498425;ENST00000495186;ENST00000446158;ENST00000414061;ENST00000466461"	"ENSP00000417052;ENSP00000390031;ENSP00000405832"	"Q15125"	"EBP"	"10682"	"EBP cholestenol delta-isomerase"	"CDPX2;CHO2;CPX;CPXD"	"Endoplasmic reticulum;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000147160"	"ENST00000276101;ENST00000440401;ENST00000443056"	"ENSP00000421172;ENSP00000427523"	"Q6E213"	"AWAT2"	"158835"	"acyl-CoA wax alcohol acyltransferase 2"	"DGAT2L4;MFAT"	"Endoplasmic reticulum"	"SwissProt"
-"ENSG00000147162"	"ENST00000488174;ENST00000373719;ENST00000373701;ENST00000472270;ENST00000498566;ENST00000444774;ENST00000455587;ENST00000459760;ENST00000462638;ENST00000466181;ENST00000474633"	"ENSP00000362824;ENSP00000362805;ENSP00000399729"	"O15294"	"OGT"	"8473"	"O-linked N-acetylglucosamine (GlcNAc) transferase"	"FLJ23071;HRNT1;MGC22921;O-GLCNAC;OGT1"	"Mitochondria;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000147224"	"ENST00000675304;ENST00000643795;ENST00000645638;ENST00000372418;ENST00000646815;ENST00000644642;ENST00000372435;ENST00000674826;ENST00000372419;ENST00000645903;ENST00000674525;ENST00000676092;ENST00000674843;ENST00000675720;ENST00000675046;ENST00000675921;ENST00000675630;ENST00000675124;ENST00000675082;ENST00000675353;ENST00000676365;ENST00000675875;ENST00000372428;ENST00000676322;ENST00000675263"	"ENSP00000496286;ENSP00000496554;ENSP00000361495;ENSP00000495801;ENSP00000495493;ENSP00000361512;ENSP00000502278;ENSP00000361496;ENSP00000502780;ENSP00000502260;ENSP00000501721;ENSP00000501767;ENSP00000502707;ENSP00000502050;ENSP00000502439;ENSP00000502347;ENSP00000502149;ENSP00000501550;ENSP00000502070;ENSP00000361505;ENSP00000501977;ENSP00000502081"	"P60891"	"PRPS1"	"5631"	"phosphoribosyl pyrophosphate synthetase 1"	"CMTX5;DFN2;DFNX1"	"Cytosol;Nucleus"	"DeepLoc2"
 "ENSG00000147383"	"ENST00000370274;ENST00000432467;ENST00000440023"	"ENSP00000359297;ENSP00000396266;ENSP00000391854"	"Q15738"	"NSDHL"	"50814"	"NAD(P) dependent steroid dehydrogenase-like"	"H105e3;SDR31E1;XAP104"	"Endoplasmic reticulum"	"SwissProt;CellAtlas"
 "ENSG00000147408"	"ENST00000454498;ENST00000332246;ENST00000397998;ENST00000522854;ENST00000518542;ENST00000519222;ENST00000523262;ENST00000517494;ENST00000520003;ENST00000524213;ENST00000517651;ENST00000523227;ENST00000522732;ENST00000522573;ENST00000523919;ENST00000524112"	"ENSP00000411816;ENSP00000330805;ENSP00000381084;ENSP00000429809;ENSP00000428216;ENSP00000428089;ENSP00000429130;ENSP00000428774;ENSP00000427740"	"Q8TDX6"	"CSGALNACT1"	"55790"	"chondroitin sulfate N-acetylgalactosaminyltransferase 1"	"ChGn;CSGalNAcT-1;FLJ11264"	"Golgi apparatus;Cytosol"	"SwissProt;CellAtlas"
@@ -2291,7 +2288,6 @@
 "ENSG00000175548"	"ENST00000308742;ENST00000551464;ENST00000553138;ENST00000548240"	"ENSP00000310120;ENSP00000448819;ENSP00000449210"	"Q5I7T1"	"ALG10B"	"144245"	"ALG10 alpha-1,2-glucosyltransferase B"	"KCR1"	"Endoplasmic reticulum"	"CellAtlas"
 "ENSG00000175564"	"ENST00000314032;ENST00000545271;ENST00000426995;ENST00000544614"	"ENSP00000323740;ENSP00000392143;ENSP00000445279"	"P55916"	"UCP3"	"7352"	"uncoupling protein 3"	"SLC25A9"	"Nucleus;Cytosol;Inner mitochondria"	"SwissProt;CellAtlas"
 "ENSG00000175567"	"ENST00000663595;ENST00000310473;ENST00000536983;ENST00000544615;ENST00000545212;ENST00000545562;ENST00000543714;ENST00000539764;ENST00000542615;ENST00000541027;ENST00000539330"	"ENSP00000499695;ENSP00000312029;ENSP00000441147;ENSP00000439706;ENSP00000438230"	"P55851"	"UCP2"	"7351"	"uncoupling protein 2"	"BMIQ4;SLC25A8"	"Inner mitochondria"	"SwissProt;CellAtlas"
-"ENSG00000175711"	"ENST00000572977;ENST00000572267;ENST00000573363;ENST00000570947;ENST00000576599;ENST00000320865;ENST00000571301;ENST00000571394;ENST00000571954;ENST00000573629;ENST00000571218"	"ENSP00000459327;ENSP00000461127;ENSP00000319979;ENSP00000458682"	"Q67FW5"	"B3GNTL1"	"146712"	"UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase like 1"	"B3GNT8"	"Nucleus"	"CellAtlas"
 "ENSG00000175806"	"ENST00000317173;ENST00000441698;ENST00000518255;ENST00000521209;ENST00000522907;ENST00000528246;ENST00000523637;ENST00000382490;ENST00000521686;ENST00000517594"	"ENSP00000313921;ENSP00000410912;ENSP00000429461;ENSP00000435644;ENSP00000428214;ENSP00000436839;ENSP00000371930;ENSP00000427725"	"Q9UJ68"	"MSRA"	"4482"	"methionine sulfoxide reductase A"	""	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000175809"	"ENST00000323684"	"ENSP00000323348"	"Q8N7E2"	"CBLL2"	"158506"	"Cbl proto-oncogene like 2"	"CT138;FLJ25735;HAKAIL;ZNF645"	"Cytosol"	"SwissProt"
 "ENSG00000175893"	"ENST00000380916;ENST00000497966"	"ENSP00000370303"	"Q8IVQ6"	"ZDHHC21"	"340481"	"zinc finger DHHC-type palmitoyltransferase 21"	"DHHC21;DNZ1;HSPC097"	"Golgi apparatus;Cytosol"	"SwissProt;CellAtlas"