diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 53204379..63873688 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -68983,7 +68983,7 @@ - MAM02945e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000090402 or ENSG00000171298 or ENSG00000214013 or ENSG00000257335" + - gene_reaction_rule: "ENSG00000090402 or ENSG00000214013 or ENSG00000257335" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.10;3.2.1.20;3.2.1.48" @@ -69038,7 +69038,7 @@ - MAM02040e: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000102393 or ENSG00000170266 or ENSG00000241343" + - gene_reaction_rule: "ENSG00000102393 or ENSG00000170266" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.2.1.22;3.2.1.23" @@ -69117,7 +69117,7 @@ - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.3" - - references: "PMID:33715524" + - references: "PMID:33715524;PMID:246961;PMID:19158351" - subsystem: - "Galactose metabolism" - confidence_score: 0 @@ -69167,7 +69167,7 @@ - MAM02555c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000085662 or ENSG00000198074" + - gene_reaction_rule: "ENSG00000085662" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.21" @@ -69281,7 +69281,7 @@ - MAM02555c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000085662 or ENSG00000198074" + - gene_reaction_rule: "ENSG00000085662" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.21" @@ -69300,7 +69300,7 @@ - MAM02917c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456" + - gene_reaction_rule: "ENSG00000116199" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.-" @@ -69319,7 +69319,7 @@ - MAM02039c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456" + - gene_reaction_rule: "ENSG00000167363 or ENSG00000172456" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.-" @@ -69357,7 +69357,7 @@ - MAM02454c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456" + - gene_reaction_rule: "ENSG00000116199" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.1.-" @@ -69406,7 +69406,7 @@ - MAM02455c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000100413 or ENSG00000100417 or ENSG00000140650" + - gene_reaction_rule: "ENSG00000100417 or ENSG00000140650" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "5.4.2.8" @@ -69425,7 +69425,7 @@ - MAM02751c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000164068 or ENSG00000173540" + - gene_reaction_rule: "ENSG00000173540" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.7.22;2.7.7.13" @@ -69499,7 +69499,7 @@ - MAM02759c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000116783 or ENSG00000254685" + - gene_reaction_rule: "ENSG00000254685" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.7.7.30" @@ -223305,7 +223305,7 @@ - rxnNotes: "" - rxnFrom: "Recon3D" - eccodes: "2.7.1.3" - - references: "PMID:33715524" + - references: "PMID:33715524;PMID:2469615;PMID:19158351" - subsystem: - "Galactose metabolism" - confidence_score: 0 @@ -307292,9 +307292,6 @@ - !!omap - id: "ENSG00000116771" - name: "AGMAT" - - !!omap - - id: "ENSG00000116783" - - name: "TNNI3K" - !!omap - id: "ENSG00000116791" - name: "CRYZ" @@ -313025,9 +313022,6 @@ - !!omap - id: "ENSG00000241119" - name: "UGT1A9" - - !!omap - - id: "ENSG00000241343" - - name: "RPL36A" - !!omap - id: "ENSG00000241360" - name: "PDXP" diff --git a/model/genes.tsv b/model/genes.tsv index c7c3f9e9..2580393e 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -884,7 +884,6 @@ ENSG00000116745 ENST00000262340 ENSP00000262340 Q16518 RPE65 6121 retinoid isome ENSG00000116748 "ENST00000637080;ENST00000520113;ENST00000369538;ENST00000639274;ENST00000639077;ENST00000638214;ENST00000485564" "ENSP00000489753;ENSP00000430075;ENSP00000358551" P23109 AMPD1 270 adenosine monophosphate deaminase 1 "MAD;MADA" "Cytosol;Nucleus" DeepLoc2 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 -ENSG00000116783 "ENST00000326637;ENST00000530184;ENST00000497284;ENST00000526236;ENST00000534020;ENST00000525480;ENST00000370889;ENST00000465473" "ENSP00000322251;ENSP00000431465;ENSP00000434975;ENSP00000433550" Q59H18 TNNI3K 51086 TNNI3 interacting kinase CARK "Cytosol;Nucleus" SwissProt 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 @@ -2778,7 +2777,6 @@ ENSG00000240857 "ENST00000381249;ENST00000468071" ENSP00000370648 Q9HBH5 RDH14 5 ENSG00000240891 "ENST00000636933;ENST00000393934;ENST00000477665;ENST00000468174;ENST00000474484" "ENSP00000490816;ENSP00000377511;ENSP00000420686" Q0VAA5 PLCXD2 257068 phosphatidylinositol specific phospholipase C X domain containing 2 FLJ31579 Nucleus CellAtlas ENSG00000240972 "ENST00000215754;ENST00000465752;ENST00000498385" ENSP00000215754 P14174 MIF 4282 macrophage migration inhibitory factor "GIF;GLIF" "Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000241119 ENST00000354728 ENSP00000346768 O60656 UGT1A9 54600 UDP glucuronosyltransferase family 1 member A9 "HLUGP4;LUGP4;UGT1AI" Endoplasmic reticulum SwissProt -ENSG00000241343 "ENST00000427805;ENST00000614077;ENST00000392994;ENST00000491851;ENST00000465340;ENST00000553110;ENST00000372849;ENST00000465744;ENST00000471855;ENST00000489407" "ENSP00000404375;ENSP00000483017;ENSP00000397659;ENSP00000446503;ENSP00000361940;ENSP00000473451" P83881 RPL36A 6173 ribosomal protein L36a "L36A;RPL44" "Endoplasmic reticulum;Cytosol" "SwissProt;CellAtlas" ENSG00000241360 "ENST00000215904;ENST00000403251" "ENSP00000215904;ENSP00000385336" Q96GD0 PDXP 57026 pyridoxal phosphatase "CIN;dJ37E16.5;FLJ32703" Cytosol SwissProt ENSG00000241404 "ENST00000333845;ENST00000395512;ENST00000432129;ENST00000466239;ENST00000482938;ENST00000489721" "ENSP00000333380;ENSP00000378888;ENSP00000401694" Q99944 EGFL8 80864 EGF like domain multiple 8 "C6orf8;NG3" Nucleus CellAtlas ENSG00000241468 "ENST00000466753;ENST00000414062;ENST00000449683;ENST00000491560;ENST00000359832;ENST00000292475;ENST00000488775;ENST00000394186;ENST00000481899;ENST00000523680;ENST00000485011;ENST00000524321" "ENSP00000412149;ENSP00000407540;ENSP00000352890;ENSP00000292475;ENSP00000418197;ENSP00000377740;ENSP00000430398" P56134 ATP5MF 9551 ATP synthase membrane subunit f "ATP5J2;ATP5JL" "Nucleus;Inner mitochondria" "SwissProt;CellAtlas"