fix: remove non-associated genes (#939)

* fix: remove unassociated genes * chore: add macaw test result --------- Co-authored-by: edkerk <[email protected]>
SysBioChalmers · Dec 22, 2024 · 1a562ce · 1a562ce
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diff --git a/data/testResults/README.md b/data/testResults/README.md
@@ -4,7 +4,7 @@ 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 #883** (MACAW)
+- **PR #939** (MACAW)
 - **PR #883** (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/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -263003,9 +263003,6 @@
     - !!omap
       - id: "ENSG00000116791"
       - name: "CRYZ"
-    - !!omap
-      - id: "ENSG00000116882"
-      - name: "HAO2"
     - !!omap
       - id: "ENSG00000116906"
       - name: "GNPAT"
@@ -263417,9 +263414,6 @@
     - !!omap
       - id: "ENSG00000124299"
       - name: "PEPD"
-    - !!omap
-      - id: "ENSG00000124302"
-      - name: "CHST8"
     - !!omap
       - id: "ENSG00000124356"
       - name: "STAMBP"
@@ -263948,9 +263942,6 @@
     - !!omap
       - id: "ENSG00000133027"
       - name: "PEMT"
-    - !!omap
-      - id: "ENSG00000133048"
-      - name: "CHI3L1"
     - !!omap
       - id: "ENSG00000133056"
       - name: "PIK3C2B"
@@ -266096,9 +266087,6 @@
     - !!omap
       - id: "ENSG00000163659"
       - name: "TIPARP"
-    - !!omap
-      - id: "ENSG00000163684"
-      - name: "RPP14"
     - !!omap
       - id: "ENSG00000163686"
       - name: "ABHD6"
@@ -267272,9 +267260,6 @@
     - !!omap
       - id: "ENSG00000175198"
       - name: "PCCA"
-    - !!omap
-      - id: "ENSG00000175229"
-      - name: "GAL3ST3"
     - !!omap
       - id: "ENSG00000175264"
       - name: "CHST1"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -884,7 +884,6 @@
 "ENSG00000116761"	"ENST00000411986;ENST00000370938;ENST00000464926;ENST00000346806;ENST00000482383"	"ENSP00000413407;ENSP00000359976;ENSP00000311554"	"P32929"	"CTH"	"1491"	"cystathionine gamma-lyase"	""	"Cytosol"	"SwissProt"
 "ENSG00000116771"	"ENST00000375826"	"ENSP00000364986"	"Q9BSE5"	"AGMAT"	"79814"	"agmatinase"	"FLJ23384"	"Mitochondria"	"DeepLoc2"
 "ENSG00000116791"	"ENST00000370872;ENST00000340866;ENST00000492102;ENST00000417775;ENST00000370871;ENST00000370870;ENST00000441120"	"ENSP00000359909;ENSP00000339399;ENSP00000399805;ENSP00000359908;ENSP00000359907;ENSP00000404289"	"Q08257"	"CRYZ"	"1429"	"crystallin zeta"	""	"Cytosol"	"SwissProt;CellAtlas"
-"ENSG00000116882"	"ENST00000457318;ENST00000361035;ENST00000325945;ENST00000482991;ENST00000622548"	"ENSP00000393955;ENSP00000354314;ENSP00000316339;ENSP00000483507"	"Q9NYQ3"	"HAO2"	"51179"	"hydroxyacid oxidase 2"	"GIG16;HAOX2"	"Peroxisome;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000116906"	"ENST00000436239;ENST00000366647;ENST00000416000;ENST00000644483;ENST00000492459;ENST00000469332"	"ENSP00000402811;ENSP00000355607;ENSP00000411640;ENSP00000496537"	"O15228"	"GNPAT"	"8443"	"glyceronephosphate O-acyltransferase"	"DAP-AT;DAPAT;DHAPAT"	"Peroxisome"	"SwissProt"
 "ENSG00000116981"	"ENST00000235628"	"ENSP00000235628"	"Q9BXI3"	"NT5C1A"	"84618"	"5'-nucleotidase, cytosolic IA"	"CN-I;CN-IA;CN1;CN1A;MGC119199;MGC119201"	"Cytosol"	"SwissProt"
 "ENSG00000116984"	"ENST00000680454;ENST00000366577;ENST00000674797;ENST00000652435;ENST00000679569;ENST00000650888;ENST00000463959;ENST00000535889;ENST00000651455;ENST00000681102;ENST00000679842;ENST00000681177;ENST00000681937;ENST00000366576;ENST00000470570;ENST00000681813;ENST00000652483"	"ENSP00000355536;ENSP00000502299;ENSP00000505932;ENSP00000498393;ENSP00000505498;ENSP00000441845;ENSP00000498963;ENSP00000505600;ENSP00000506109;ENSP00000506327;ENSP00000355535"	"Q99707"	"MTR"	"4548"	"5-methyltetrahydrofolate-homocysteine methyltransferase"	"cblG"	"Cytosol"	"SwissProt;CellAtlas"
@@ -1022,7 +1021,6 @@
 "ENSG00000124253"	"ENST00000467047;ENST00000319441;ENST00000475833;ENST00000498194;ENST00000470051;ENST00000485958"	"ENSP00000319814"	"P35558"	"PCK1"	"5105"	"phosphoenolpyruvate carboxykinase 1"	"PEPCK-C"	"Cytosol;Endoplasmic reticulum"	"SwissProt"
 "ENSG00000124275"	"ENST00000507837;ENST00000502509;ENST00000511639;ENST00000513439;ENST00000264668;ENST00000508047;ENST00000510279;ENST00000514220;ENST00000511461;ENST00000503550;ENST00000440940;ENST00000514369;ENST00000502550;ENST00000506877;ENST00000512217;ENST00000510525;ENST00000508890;ENST00000508101;ENST00000509961;ENST00000512311;ENST00000507414;ENST00000507202;ENST00000508354;ENST00000506115;ENST00000509379"	"ENSP00000426710;ENSP00000264668;ENSP00000423139;ENSP00000427200;ENSP00000423863;ENSP00000424719;ENSP00000424644;ENSP00000402510;ENSP00000426132;ENSP00000424599;ENSP00000427416;ENSP00000421318;ENSP00000421991"	"Q9UBK8"	"MTRR"	"4552"	"5-methyltetrahydrofolate-homocysteine methyltransferase reductase"	"cblE"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000124299"	"ENST00000593085;ENST00000244137;ENST00000588328;ENST00000591968;ENST00000397032;ENST00000436370;ENST00000651901;ENST00000590731;ENST00000609145;ENST00000588719;ENST00000651646;ENST00000590755;ENST00000590408;ENST00000593163"	"ENSP00000244137;ENSP00000468516;ENSP00000380226;ENSP00000391890;ENSP00000498922;ENSP00000498950;ENSP00000476667;ENSP00000476869"	"P12955"	"PEPD"	"5184"	"peptidase D"	""	"Nucleus"	"CellAtlas"
-"ENSG00000124302"	"ENST00000591231;ENST00000438847;ENST00000604556;ENST00000262622;ENST00000650847;ENST00000434302"	"ENSP00000467012;ENSP00000393879;ENSP00000262622;ENSP00000499084;ENSP00000392604"	"Q9H2A9"	"CHST8"	"64377"	"carbohydrate sulfotransferase 8"	"GALNAC-4-ST1"	"Golgi apparatus"	"SwissProt"
 "ENSG00000124356"	"ENST00000339566;ENST00000683349;ENST00000682157;ENST00000683036;ENST00000683317;ENST00000682847;ENST00000684095;ENST00000684337;ENST00000683247;ENST00000682329;ENST00000682683;ENST00000683149;ENST00000682851;ENST00000683728;ENST00000394070;ENST00000409707;ENST00000684585;ENST00000683434;ENST00000682352;ENST00000684697;ENST00000682592;ENST00000683718;ENST00000683518;ENST00000424659;ENST00000536064;ENST00000684200;ENST00000684355;ENST00000684774;ENST00000478946;ENST00000682423;ENST00000683465;ENST00000682998;ENST00000682799;ENST00000684703;ENST00000683016;ENST00000684174;ENST00000684716;ENST00000394073;ENST00000684671;ENST00000682848;ENST00000683877;ENST00000683530;ENST00000683027;ENST00000683304;ENST00000684321;ENST00000683852;ENST00000684312;ENST00000682379;ENST00000683205;ENST00000682784;ENST00000682351;ENST00000683818;ENST00000684426;ENST00000683582;ENST00000452725;ENST00000682105;ENST00000683594;ENST00000682387;ENST00000682747;ENST00000683417;ENST00000683928;ENST00000683391;ENST00000684758;ENST00000682558;ENST00000432295;ENST00000683902;ENST00000486458;ENST00000683314;ENST00000682271;ENST00000683408;ENST00000487811"	"ENSP00000344742;ENSP00000507807;ENSP00000507848;ENSP00000507639;ENSP00000507092;ENSP00000507864;ENSP00000506845;ENSP00000508310;ENSP00000507237;ENSP00000507540;ENSP00000507371;ENSP00000507079;ENSP00000377633;ENSP00000386548;ENSP00000507054;ENSP00000507622;ENSP00000508197;ENSP00000506855;ENSP00000508170;ENSP00000507037;ENSP00000506865;ENSP00000390921;ENSP00000443502;ENSP00000507468;ENSP00000507974;ENSP00000508267;ENSP00000508259;ENSP00000507643;ENSP00000507046;ENSP00000507089;ENSP00000507569;ENSP00000508373;ENSP00000508172;ENSP00000377636;ENSP00000507882;ENSP00000506775;ENSP00000507446;ENSP00000506920;ENSP00000508114;ENSP00000507156;ENSP00000507717;ENSP00000506958;ENSP00000507081;ENSP00000507523;ENSP00000506833;ENSP00000507658;ENSP00000507614;ENSP00000506892;ENSP00000507182;ENSP00000507459;ENSP00000508186;ENSP00000507770;ENSP00000507241;ENSP00000506772;ENSP00000507279;ENSP00000507014;ENSP00000413874;ENSP00000507096"	"O95630"	"STAMBP"	"10617"	"STAM binding protein"	"AMSH"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000124357"	"ENST00000531799;ENST00000497690;ENST00000455662;ENST00000531934;ENST00000455197;ENST00000418807;ENST00000443872;ENST00000443938;ENST00000484984;ENST00000244204;ENST00000493102;ENST00000450272;ENST00000465105;ENST00000480411;ENST00000475709;ENST00000533981;ENST00000472519;ENST00000489309;ENST00000464638;ENST00000428360;ENST00000524736;ENST00000479854;ENST00000529236;ENST00000478659;ENST00000524537;ENST00000490998;ENST00000468601;ENST00000498022;ENST00000613852"	"ENSP00000389087;ENSP00000436326;ENSP00000408550;ENSP00000396070;ENSP00000404531;ENSP00000411846;ENSP00000244204;ENSP00000400941;ENSP00000435207;ENSP00000435437;ENSP00000431204;ENSP00000437192;ENSP00000477639"	"Q9UJ70"	"NAGK"	"55577"	"N-acetylglucosamine kinase"	"GNK"	"Cytosol;Nucleus"	"CellAtlas"
 "ENSG00000124370"	"ENST00000413592;ENST00000244217;ENST00000462609;ENST00000494660;ENST00000486135"	"ENSP00000391140;ENSP00000244217;ENSP00000437361;ENSP00000441569"	"Q96PE7"	"MCEE"	"84693"	"methylmalonyl-CoA epimerase"	"GLOD2;MCE"	"Mitochondria;Nucleus"	"SwissProt;CellAtlas"
@@ -1199,7 +1197,6 @@
 "ENSG00000132915"	"ENST00000255266;ENST00000508173;ENST00000512670;ENST00000613228;ENST00000617647"	"ENSP00000255266;ENSP00000478060;ENSP00000482774"	"P16499"	"PDE6A"	"5145"	"phosphodiesterase 6A"	"PDEA;RP43"	"Cytosol"	"SwissProt"
 "ENSG00000132958"	"ENST00000382978;ENST00000462409;ENST00000390680;ENST00000400103;ENST00000400230;ENST00000255310"	"ENSP00000372438;ENSP00000432402;ENSP00000375098;ENSP00000382974;ENSP00000383089;ENSP00000255310"	"Q6XPS3"	"TPTE2"	"93492"	"transmembrane phosphoinositide 3-phosphatase and tensin homolog 2"	"TPIP"	"Endoplasmic reticulum;Golgi apparatus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000133027"	"ENST00000582268;ENST00000484838;ENST00000490392;ENST00000395782;ENST00000395783;ENST00000435340;ENST00000255389;ENST00000395781;ENST00000477595;ENST00000580147;ENST00000421096;ENST00000472446;ENST00000461404"	"ENSP00000379128;ENSP00000379129;ENSP00000391288;ENSP00000255389;ENSP00000379127;ENSP00000463112;ENSP00000463713"	"Q9UBM1"	"PEMT"	"10400"	"phosphatidylethanolamine N-methyltransferase"	"PEMPT;PEMT2"	"Endoplasmic reticulum;Mitochondria;Cytosol"	"SwissProt;CellAtlas"
-"ENSG00000133048"	"ENST00000473185;ENST00000255409;ENST00000404436;ENST00000478742;ENST00000472064"	"ENSP00000255409;ENSP00000385350"	"P36222"	"CHI3L1"	"1116"	"chitinase 3 like 1"	"GP39;YK-40;YKL40"	"Endoplasmic reticulum;Golgi apparatus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000133056"	"ENST00000367187;ENST00000424712;ENST00000684373;ENST00000683234;ENST00000462752;ENST00000479079;ENST00000496872;ENST00000415899;ENST00000367184;ENST00000429009"	"ENSP00000356155;ENSP00000400561;ENSP00000507222;ENSP00000401795;ENSP00000356152;ENSP00000409554"	"O00750"	"PIK3C2B"	"5287"	"phosphatidylinositol-4-phosphate 3-kinase catalytic subunit type 2 beta"	"C2-PI3K;PI3K-C2beta"	"Endoplasmic reticulum;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000133063"	"ENST00000484834;ENST00000479483;ENST00000367229;ENST00000491855;ENST00000255427;ENST00000503786;ENST00000506427;ENST00000513472;ENST00000460619"	"ENSP00000356198;ENSP00000423778;ENSP00000255427;ENSP00000421617"	"Q13231"	"CHIT1"	"1118"	"chitinase 1"	"CHI3;CHIT"	"Lysosome"	"SwissProt"
 "ENSG00000133065"	"ENST00000367137;ENST00000468057;ENST00000484228;ENST00000484000"	"ENSP00000356105"	"Q8IVJ1"	"SLC41A1"	"254428"	"solute carrier family 41 member 1"	"MgtE"	"Mitochondria"	"CellAtlas"
@@ -1908,7 +1905,6 @@
 "ENSG00000163631"	"ENST00000441319;ENST00000295897;ENST00000510166;ENST00000515133;ENST00000415165;ENST00000514786;ENST00000476441;ENST00000503124;ENST00000509063;ENST00000401494;ENST00000505649;ENST00000511370;ENST00000507673;ENST00000484992;ENST00000504043;ENST00000486939;ENST00000508932;ENST00000495173;ENST00000621085;ENST00000621628"	"ENSP00000392541;ENSP00000295897;ENSP00000401820;ENSP00000423727;ENSP00000421027;ENSP00000422784;ENSP00000384695;ENSP00000426179;ENSP00000483421;ENSP00000480485"	"P02768"	"ALB"	"213"	"albumin"	""	"Endoplasmic reticulum;Golgi apparatus"	"CellAtlas"
 "ENSG00000163655"	"ENST00000496455;ENST00000295920;ENST00000476145"	"ENSP00000419851;ENSP00000295920"	"P49915"	"GMPS"	"8833"	"guanine monophosphate synthase"	"GATD7"	"Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000163659"	"ENST00000486483;ENST00000295924;ENST00000461166;ENST00000473702;ENST00000481853;ENST00000495891;ENST00000542783"	"ENSP00000418757;ENSP00000295924;ENSP00000420612;ENSP00000419982;ENSP00000418829;ENSP00000420141;ENSP00000438345"	"Q7Z3E1"	"TIPARP"	"25976"	"TCDD inducible poly(ADP-ribose) polymerase"	"ARTD14;DDF1;DKFZP434J214;DKFZp686N0351;PARP-1;PARP-7;PARP7;pART14;RM1"	"Nucleus"	"SwissProt"
-"ENSG00000163684"	"ENST00000295959;ENST00000461797;ENST00000445193;ENST00000466547;ENST00000463550;ENST00000462046"	"ENSP00000295959;ENSP00000412894;ENSP00000419909"	"O95059"	"RPP14"	"11102"	"ribonuclease P/MRP subunit p14"	"P14"	"Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000163686"	"ENST00000295962;ENST00000478253;ENST00000475982;ENST00000463756;ENST00000485900;ENST00000470440;ENST00000480457"	"ENSP00000295962;ENSP00000420315;ENSP00000418209;ENSP00000420408;ENSP00000418934"	"Q9BV23"	"ABHD6"	"57406"	"abhydrolase domain containing 6, acylglycerol lipase"	""	"Nucleus;Lysosome"	"SwissProt;CellAtlas"
 "ENSG00000163719"	"ENST00000353332;ENST00000420925;ENST00000447144;ENST00000430020;ENST00000296003;ENST00000351233;ENST00000416864;ENST00000437997;ENST00000480578;ENST00000449543;ENST00000414996;ENST00000431250;ENST00000606184"	"ENSP00000323462;ENSP00000401993;ENSP00000410761;ENSP00000392690;ENSP00000296003;ENSP00000334070;ENSP00000412644;ENSP00000408813;ENSP00000411417;ENSP00000392935;ENSP00000388746"	"Q8NCE2"	"MTMR14"	"64419"	"myotubularin related protein 14"	"C3orf29;FLJ22405;FLJ90311;hEDTP;hJumpy"	"Cytosol;Nucleus"	"SwissProt"
 "ENSG00000163738"	"ENST00000429519;ENST00000490698;ENST00000475291;ENST00000429335;ENST00000433372;ENST00000423607;ENST00000395759;ENST00000461101;ENST00000325278;ENST00000359107;ENST00000484725;ENST00000492183;ENST00000461856;ENST00000465255;ENST00000490128"	"ENSP00000391327;ENSP00000409391;ENSP00000405692;ENSP00000387614;ENSP00000379108;ENSP00000321984;ENSP00000352012"	"Q9H903"	"MTHFD2L"	"441024"	"methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2 like"	"MGC72244"	"Inner mitochondria"	"SwissProt"
@@ -2294,7 +2290,6 @@
 "ENSG00000175066"	"ENST00000392993;ENST00000492097;ENST00000480757;ENST00000460515;ENST00000463349;ENST00000486459;ENST00000460630;ENST00000460544;ENST00000487672;ENST00000466685;ENST00000472759;ENST00000489085"	"ENSP00000418001;ENSP00000420312;ENSP00000419031;ENSP00000417153;ENSP00000420593;ENSP00000418239"	"Q6ZS86"	"GK5"	"256356"	"glycerol kinase 5"	"MGC40579"	"Cytosol;Nucleus"	"CellAtlas"
 "ENSG00000175164"	"ENST00000679909;ENST00000680600;ENST00000453660;ENST00000647353;ENST00000611156;ENST00000538324;ENST00000651471"	"ENSP00000506089;ENSP00000483265;ENSP00000483018"	"A0A087X009"	"ABO"	"28"	"ABO, alpha 1-3-N-acetylgalactosaminyltransferase and alpha 1-3-galactosyltransferase"	"A3GALNT;A3GALT1"	"Golgi apparatus"	"DeepLoc2"
 "ENSG00000175198"	"ENST00000376285;ENST00000647303;ENST00000637358;ENST00000636420;ENST00000636366;ENST00000636475;ENST00000637657;ENST00000485946;ENST00000424527;ENST00000443601;ENST00000458283;ENST00000413170;ENST00000621936;ENST00000428969;ENST00000376286;ENST00000376279"	"ENSP00000365462;ENSP00000495663;ENSP00000489804;ENSP00000490290;ENSP00000490939;ENSP00000490843;ENSP00000489974;ENSP00000396050;ENSP00000400740;ENSP00000390850;ENSP00000411194;ENSP00000399413;ENSP00000365463;ENSP00000365456"	"P05165"	"PCCA"	"5095"	"propionyl-CoA carboxylase subunit alpha"	""	"Mitochondria"	"SwissProt;CellAtlas"
-"ENSG00000175229"	"ENST00000312006;ENST00000527878;ENST00000527048"	"ENSP00000308591;ENSP00000434829"	"Q96A11"	"GAL3ST3"	"89792"	"galactose-3-O-sulfotransferase 3"	"GAL3ST2"	"Golgi apparatus"	"SwissProt"
 "ENSG00000175264"	"ENST00000308064;ENST00000533673;ENST00000531322"	"ENSP00000309270"	"O43916"	"CHST1"	"8534"	"carbohydrate sulfotransferase 1"	"C6ST;KSGal6ST"	"Golgi apparatus"	"SwissProt"
 "ENSG00000175283"	"ENST00000372586"	"ENSP00000361667"	"Q9UPQ8"	"DOLK"	"22845"	"dolichol kinase"	"DK1;KIAA1094;TMEM15"	"Endoplasmic reticulum;Nucleus;Cytosol"	"SwissProt;CellAtlas"
 "ENSG00000175309"	"ENST00000308158;ENST00000481436;ENST00000481811;ENST00000489262;ENST00000474052;ENST00000393488;ENST00000493197;ENST00000494126;ENST00000510991;ENST00000476487;ENST00000506045;ENST00000510913;ENST00000504096;ENST00000514424;ENST00000323594;ENST00000506001;ENST00000511716;ENST00000476170"	"ENSP00000310978;ENSP00000423806;ENSP00000377128;ENSP00000425425;ENSP00000427444;ENSP00000424608;ENSP00000321290;ENSP00000421810"	"Q8IUZ5"	"PHYKPL"	"85007"	"5-phosphohydroxy-L-lysine phospho-lyase"	"AGXT2L2;MGC15875"	"Mitochondria"	"SwissProt;CellAtlas"