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fix: remove non-metabolic genes from Fructose and mannose metabolism #461

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Jan 24, 2023
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fix: remove non-metabolic genes from Fructose and mannose metabolism #461

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14 changes: 4 additions & 10 deletions model/Human-GEM.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@
short_name: "Human-GEM"
full_name: "Generic genome-scale metabolic model of Homo sapiens"
version: ""
date: "2023-01-17"
date: "2023-01-23"
authors: "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas"
email: "jonrob@chalmers.se"
organization: "Chalmers University of Technology"
Expand Down Expand Up @@ -68785,7 +68785,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000144591 or ENSG00000164068 or ENSG00000173540 or ENSG00000176020"
- gene_reaction_rule: "ENSG00000164068 or ENSG00000173540"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.7.22;2.7.7.13"
Expand All @@ -68804,7 +68804,7 @@
- MAM02759c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000144591 or ENSG00000173540 or ENSG00000176020"
- gene_reaction_rule: "ENSG00000173540"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.7.13"
Expand Down Expand Up @@ -68931,7 +68931,7 @@
- MAM02751c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000078237 or ENSG00000108813 or ENSG00000114268 or ENSG00000123836 or ENSG00000158571 or ENSG00000170525"
- gene_reaction_rule: "ENSG00000078237 or ENSG00000114268 or ENSG00000123836 or ENSG00000158571 or ENSG00000170525"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.1.3.46;3.1.3.11"
Expand Down Expand Up @@ -306441,8 +306441,6 @@
- id: "ENSG00000108786"
- !!omap
- id: "ENSG00000108799"
- !!omap
- id: "ENSG00000108813"
- !!omap
- id: "ENSG00000108839"
- !!omap
Expand Down Expand Up @@ -308259,8 +308257,6 @@
- id: "ENSG00000144401"
- !!omap
- id: "ENSG00000144583"
- !!omap
- id: "ENSG00000144591"
- !!omap
- id: "ENSG00000144659"
- !!omap
Expand Down Expand Up @@ -309915,8 +309911,6 @@
- id: "ENSG00000175893"
- !!omap
- id: "ENSG00000175931"
- !!omap
- id: "ENSG00000176020"
- !!omap
- id: "ENSG00000176022"
- !!omap
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3 changes: 0 additions & 3 deletions model/genes.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -704,7 +704,6 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen
"ENSG00000108784" "ENST00000225927;ENST00000586516;ENST00000591587;ENST00000590358;ENST00000592454" "ENSP00000225927;ENSP00000467135;ENSP00000467836;ENSP00000466892;ENSP00000468665" "P54802" "NAGLU" "4669" "N-acetyl-alpha-glucosaminidase" "NAG" "Lysosome" "SwissProt"
"ENSG00000108786" "ENST00000593215;ENST00000587280;ENST00000590299;ENST00000585807;ENST00000225929" "ENSP00000465128;ENSP00000466799;ENSP00000225929" "P14061" "HSD17B1" "3292" "hydroxysteroid 17-beta dehydrogenase 1" "EDH17B2;EDHB17;HSD17;MGC138140;SDR28C1" "Cytosol" "SwissProt;CellAtlas"
"ENSG00000108799" "ENST00000428826;ENST00000415827;ENST00000586714;ENST00000592743;ENST00000588897;ENST00000585893;ENST00000590078;ENST00000586103;ENST00000585912;ENST00000585550;ENST00000591330;ENST00000590783;ENST00000589846;ENST00000588239;ENST00000585455;ENST00000586935;ENST00000586382;ENST00000586867;ENST00000587179;ENST00000593148;ENST00000586089;ENST00000593214;ENST00000592492;ENST00000590082" "ENSP00000404658;ENSP00000407869;ENSP00000466924;ENSP00000467036;ENSP00000467871;ENSP00000465220;ENSP00000468640;ENSP00000465423;ENSP00000464753;ENSP00000465327;ENSP00000466393;ENSP00000467320;ENSP00000465482" "Q92800" "EZH1" "2145" "enhancer of zeste 1 polycomb repressive complex 2 subunit" "KIAA0388;KMT6B" "Nucleus" "SwissProt;CellAtlas"
"ENSG00000108813" "ENST00000503410;ENST00000240306;ENST00000505318;ENST00000503276;ENST00000411890;ENST00000611342" "ENSP00000240306;ENSP00000410622;ENSP00000480366" "Q92988" "DLX4" "1748" "distal-less homeobox 4" "BP1;DLX7;DLX8;DLX9" "Nucleus" "SwissProt;CellAtlas"
"ENSG00000108839" "ENST00000251535;ENST00000480801;ENST00000406228" "ENSP00000251535;ENSP00000467033" "P18054" "ALOX12" "239" "arachidonate 12-lipoxygenase, 12S type" "12S-LOX" "Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000108846" "ENST00000515707;ENST00000513511;ENST00000427699;ENST00000285238;ENST00000502426;ENST00000505699;ENST00000515585;ENST00000513589;ENST00000571855;ENST00000515070;ENST00000503304;ENST00000510633;ENST00000506464;ENST00000513745;ENST00000510891;ENST00000503337;ENST00000508929;ENST00000504586" "ENSP00000422786;ENSP00000425697;ENSP00000395160;ENSP00000285238;ENSP00000427073;ENSP00000427521;ENSP00000424981;ENSP00000422058;ENSP00000421755" "O15438" "ABCC3" "8714" "ATP binding cassette subfamily C member 3" "cMOAT2;EST90757;MLP2;MOAT-D;MRP3" "Cell membrane;Lysosome" "DeepLoc2"
"ENSG00000108854" "ENST00000262435;ENST00000582081;ENST00000578386;ENST00000585301;ENST00000580072;ENST00000578200;ENST00000580246" "ENSP00000262435;ENSP00000463531;ENSP00000464432;ENSP00000463804" "Q9HAU4" "SMURF2" "64750" "SMAD specific E3 ubiquitin protein ligase 2" "" "Nucleus;Cytosol" "SwissProt;CellAtlas"
Expand Down Expand Up @@ -1613,7 +1612,6 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen
"ENSG00000144362" "ENST00000616481;ENST00000616524;ENST00000617738;ENST00000359744;ENST00000438838;ENST00000438710;ENST00000449906;ENST00000476919" "ENSP00000481680;ENSP00000481046;ENSP00000481857;ENSP00000352782;ENSP00000393983;ENSP00000411844;ENSP00000416790" "Q8TCD6" "PHOSPHO2" "493911" "phosphatase, orphan 2" "MGC22679" "Nucleus" "CellAtlas"
"ENSG00000144401" "ENST00000432416;ENST00000458426;ENST00000425132;ENST00000477919;ENST00000448007;ENST00000272839;ENST00000448823;ENST00000406927;ENST00000426075;ENST00000442521;ENST00000461419;ENST00000471128;ENST00000411432" "ENSP00000416570;ENSP00000389684;ENSP00000400730;ENSP00000407622;ENSP00000272839;ENSP00000409485;ENSP00000385481;ENSP00000403317;ENSP00000392062;ENSP00000415115" "Q8WXB1" "METTL21A" "151194" "methyltransferase like 21A" "FAM119A;HCA557b;HSPA-KMT;LOC151194" "Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000144583" "ENST00000273067" "ENSP00000273067" "Q9P2E8" "MARCHF4" "57574" "membrane associated ring-CH-type finger 4" "KIAA1399;MARCH-IV;MARCH4;RNF174" "Cell membrane;Endoplasmic reticulum;Lysosome;Golgi apparatus" "DeepLoc2"
"ENSG00000144591" "ENST00000684669;ENST00000683382;ENST00000682340;ENST00000684274;ENST00000683241;ENST00000684227;ENST00000683746;ENST00000683591;ENST00000684562;ENST00000682058;ENST00000682435;ENST00000683617;ENST00000684242;ENST00000635609;ENST00000683964;ENST00000684412;ENST00000373917;ENST00000682102;ENST00000455657;ENST00000682576;ENST00000684334;ENST00000683598;ENST00000683131;ENST00000683946;ENST00000435316;ENST00000313597;ENST00000684729;ENST00000683203;ENST00000683864;ENST00000682481;ENST00000358215;ENST00000480506;ENST00000443704;ENST00000373908;ENST00000622191;ENST00000683752;ENST00000341142;ENST00000682443;ENST00000683691;ENST00000683402;ENST00000683386;ENST00000683626;ENST00000684706;ENST00000481170;ENST00000682488;ENST00000496536;ENST00000683106;ENST00000480034" "ENSP00000507011;ENSP00000507190;ENSP00000508406;ENSP00000507378;ENSP00000363027;ENSP00000508279;ENSP00000392465;ENSP00000508370;ENSP00000508168;ENSP00000507530;ENSP00000506941;ENSP00000411060;ENSP00000315925;ENSP00000507441;ENSP00000507147;ENSP00000507331;ENSP00000350949;ENSP00000396750;ENSP00000363016;ENSP00000478700;ENSP00000507197;ENSP00000340760;ENSP00000508392;ENSP00000507137;ENSP00000507844;ENSP00000507216;ENSP00000507140;ENSP00000489451" "Q96IJ6" "GMPPA" "29926" "GDP-mannose pyrophosphorylase A" "" "Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000144659" "ENST00000650617;ENST00000431510;ENST00000645630;ENST00000648579;ENST00000642683;ENST00000645280;ENST00000643672;ENST00000642978;ENST00000642442" "ENSP00000497532;ENSP00000394244;ENSP00000493714;ENSP00000497638;ENSP00000495376;ENSP00000496690;ENSP00000494532;ENSP00000494342" "Q96DW6" "SLC25A38" "54977" "solute carrier family 25 member 38" "FLJ20551" "Inner mitochondria" "SwissProt"
"ENSG00000144741" "ENST00000676754;ENST00000354883;ENST00000336733;ENST00000464350;ENST00000413054;ENST00000483224;ENST00000484768" "ENSP00000504323;ENSP00000346955;ENSP00000336801;ENSP00000432574;ENSP00000415304;ENSP00000437217" "Q70HW3" "SLC25A26" "115286" "solute carrier family 25 member 26" "" "Inner mitochondria" "SwissProt;CellAtlas"
"ENSG00000144744" "ENST00000415609;ENST00000361055;ENST00000349511;ENST00000461934;ENST00000465627;ENST00000461522;ENST00000465108;ENST00000493957;ENST00000466763;ENST00000485424;ENST00000464605;ENST00000630585;ENST00000631029" "ENSP00000400294;ENSP00000354340;ENSP00000340041;ENSP00000417547;ENSP00000419077;ENSP00000486985;ENSP00000486366" "Q8TBC4" "UBA3" "9039" "ubiquitin like modifier activating enzyme 3" "hUba3;NAE2;UBE1C" "Cytosol;Nucleus" "CellAtlas"
Expand Down Expand Up @@ -2441,7 +2439,6 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen
"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"
"ENSG00000175931" "ENST00000319380;ENST00000587127;ENST00000586409;ENST00000587581;ENST00000590658;ENST00000586505" "ENSP00000323687;ENSP00000468498;ENSP00000467623" "Q9C0C9" "UBE2O" "63893" "ubiquitin conjugating enzyme E2 O" "E2-230K" "Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000176020" "ENST00000320431" "ENSP00000323096" "Q86WK7" "AMIGO3" "386724" "adhesion molecule with Ig like domain 3" "" "Cell membrane" "DeepLoc2"
"ENSG00000176022" "ENST00000379198" "ENSP00000368496" "Q96L58" "B3GALT6" "126792" "beta-1,3-galactosyltransferase 6" "beta3GalT6" "Golgi apparatus" "SwissProt"
"ENSG00000176095" "ENST00000321599;ENST00000468463;ENST00000460540;ENST00000495798;ENST00000479464;ENST00000498149;ENST00000495152;ENST00000613416;ENST00000395238" "ENSP00000323780;ENSP00000420467;ENSP00000420762;ENSP00000482032;ENSP00000378659" "Q92551" "IP6K1" "9807" "inositol hexakisphosphate kinase 1" "IHPK1;KIAA0263" "Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000176153" "ENST00000553522;ENST00000612794;ENST00000389614;ENST00000557049;ENST00000557323" "ENSP00000450991;ENSP00000478082;ENSP00000374265;ENSP00000451721;ENSP00000451844" "P18283" "GPX2" "2877" "glutathione peroxidase 2" "GSHPX-GI" "Nucleus;Cytosol" "SwissProt;CellAtlas"
Expand Down