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Remove wrongly annotated genes for glycolysis pathway and lactate dehydrogenase #517

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merged 4 commits into from
Mar 29, 2023
Merged

Remove wrongly annotated genes for glycolysis pathway and lactate dehydrogenase #517

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1c8eacf
feat-refine GPR for glycolysis pathway
feiranl Mar 28, 2023
0bdb653
fix the GPR for lactate dehydrogenase
feiranl Mar 29, 2023
0796938
Merge branch `develop` into refine-gly
haowang-bioinfo Mar 29, 2023
f4e3b95
fix: re-delete previously removed gene
haowang-bioinfo Mar 29, 2023
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12 changes: 5 additions & 7 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: "2023-03-26"
date: "2023-03-29"
authors: "Jonathan Robinson, Hao Wang, Pierre-Etienne Cholley, Pinar Kocabas"
email: "[email protected]"
organization: "Chalmers University of Technology"
Expand Down Expand Up @@ -67064,7 +67064,7 @@
- MAM02819x: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000111716 or ENSG00000134333 or ENSG00000166796 or ENSG00000166800 or ENSG00000171989"
- gene_reaction_rule: "ENSG00000171989"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.27"
Expand Down Expand Up @@ -67178,7 +67178,7 @@
- MAM02883c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000109107 or ENSG00000136872 or ENSG00000149925"
- gene_reaction_rule: "ENSG00000109107 or ENSG00000136872"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "4.1.2.13"
Expand Down Expand Up @@ -67268,7 +67268,7 @@
- MAM01371c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000096006 or ENSG00000102144 or ENSG00000154305 or ENSG00000170950"
- gene_reaction_rule: "ENSG00000096006 or ENSG00000102144 or ENSG00000170950"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.2.3"
Expand Down Expand Up @@ -69868,7 +69868,7 @@
- MAM02819m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000111716 or ENSG00000134333 or ENSG00000166796 or ENSG00000166800 or ENSG00000171989"
- gene_reaction_rule: "ENSG00000111716 or ENSG00000171989"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.27"
Expand Down Expand Up @@ -308416,8 +308416,6 @@
- id: "ENSG00000154252"
- !!omap
- id: "ENSG00000154269"
- !!omap
- id: "ENSG00000154305"
- !!omap
- id: "ENSG00000154370"
- !!omap
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1 change: 0 additions & 1 deletion model/genes.tsv
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Expand Up @@ -1728,7 +1728,6 @@ genes geneENSTID geneENSPID geneUniProtID geneSymbols geneEntrezID geneNames gen
"ENSG00000154227" "ENST00000679737;ENST00000284382;ENST00000538112;ENST00000394113;ENST00000560944;ENST00000560348;ENST00000558884;ENST00000559023;ENST00000559639" "ENSP00000506641;ENSP00000284382;ENSP00000437640;ENSP00000377672;ENSP00000453816;ENSP00000453598" "Q8IU89" "CERS3" "204219" "ceramide synthase 3" "LASS3;MGC27091" "Endoplasmic reticulum;Nucleus" "SwissProt;CellAtlas"
"ENSG00000154252" "ENST00000192314" "ENSP00000192314" "Q9H3Q3" "GAL3ST2" "64090" "galactose-3-O-sulfotransferase 2" "GP3ST" "Golgi apparatus" "SwissProt"
"ENSG00000154269" "ENST00000427707;ENST00000414305;ENST00000423831;ENST00000470930;ENST00000494023;ENST00000357639;ENST00000358229" "ENSP00000415589;ENSP00000406261;ENSP00000408642;ENSP00000350265;ENSP00000350964" "O14638" "ENPP3" "5169" "ectonucleotide pyrophosphatase/phosphodiesterase 3" "B10;CD203c;gp130RB13-6;PD-IBETA;PDNP3" "Cell membrane" "DeepLoc2"
"ENSG00000154305" "ENST00000344922;ENST00000470521;ENST00000354906;ENST00000340535;ENST00000495210;ENST00000467190;ENST00000476400;ENST00000475451;ENST00000479370;ENST00000450260;ENST00000477519" "ENSP00000340900;ENSP00000355062;ENSP00000345866" "Q5JRA6" "MIA3" "375056" "MIA SH3 domain ER export factor 3" "FLJ39207;KIAA0268;TANGO;TANGO1;UNQ6077" "Endoplasmic reticulum" "SwissProt"
"ENSG00000154370" "ENST00000493030;ENST00000284551;ENST00000602582;ENST00000475775;ENST00000366699;ENST00000602308" "ENSP00000473360;ENSP00000284551;ENSP00000473574;ENSP00000355660;ENSP00000473579" "Q96F44" "TRIM11" "81559" "tripartite motif containing 11" "BIA1;RNF92" "Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000154447" "ENST00000284637;ENST00000511421;ENST00000508685;ENST00000502315;ENST00000510806" "ENSP00000284637;ENSP00000426418;ENSP00000427585;ENSP00000421714" "Q7Z6J0" "SH3RF1" "57630" "SH3 domain containing ring finger 1" "KIAA1494;POSH;RNF142;SH3MD2" "Cytosol;Golgi apparatus" "SwissProt"
"ENSG00000154518" "ENST00000284727;ENST00000409194;ENST00000392541;ENST00000497075;ENST00000472782" "ENSP00000284727;ENSP00000387317;ENSP00000376324" "P48201" "ATP5MC3" "518" "ATP synthase membrane subunit c locus 3" "ATP5G3" "Mitochondria" "DeepLoc2"
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