From 8186362a4e2b1e2a7c9e7bbca58d7d57d31d9af2 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Tue, 17 Dec 2024 08:45:19 +0800 Subject: [PATCH] fix-GPR_curation_for_Gly_Ser_Thr_Val_Leu_Ile_metabolism (#885) * fix-GPR_curation_for_Gly_Ser_Thr_Val_Leu_Ile_metabolism * chore: add macaw test result --------- Co-authored-by: JHL-452b Co-authored-by: Eduard Kerkhoven --- model/Human-GEM.yml | 25 +++++++++++-------------- model/genes.tsv | 1 - 2 files changed, 11 insertions(+), 15 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 00b60dbc..53204379 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -79545,7 +79545,7 @@ - MAM02181m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149124 or ENSG00000156689 or ENSG00000166840" + - gene_reaction_rule: "ENSG00000149124 or ENSG00000156689" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.13" @@ -79619,7 +79619,7 @@ - MAM02039m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000149124 or ENSG00000156689 or ENSG00000166840" + - gene_reaction_rule: "ENSG00000149124" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.13" @@ -79675,7 +79675,7 @@ - MAM02530m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000161653" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.1" @@ -79730,7 +79730,7 @@ - MAM02896c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111237 or ENSG00000146733" + - gene_reaction_rule: "ENSG00000146733" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "3.1.3.3" @@ -79827,7 +79827,7 @@ - MAM02553c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000137106" + - gene_reaction_rule: "" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.79;1.1.1.81" @@ -79900,7 +79900,7 @@ - MAM02944m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000023330 or ENSG00000158578 or ENSG00000178773" + - gene_reaction_rule: "ENSG00000023330 or ENSG00000178773" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.3.1.37" @@ -80385,7 +80385,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000101323 or ENSG00000116882" + - gene_reaction_rule: "ENSG00000101323" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.3.15" @@ -82228,7 +82228,7 @@ - MAM02553m: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000072506 or ENSG00000106049 or ENSG00000138796" + - gene_reaction_rule: "ENSG00000072506 or ENSG00000106049" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.31;1.1.1.35" @@ -82468,7 +82468,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000179148 or ENSG00000179477 or ENSG00000188676" + - gene_reaction_rule: "ENSG00000179148 or ENSG00000179477" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.13.11.-" @@ -82487,7 +82487,7 @@ - MAM02553c: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857" + - gene_reaction_rule: "ENSG00000100867 or ENSG00000109854 or ENSG00000138400 or ENSG00000145439 or ENSG00000159692 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000204228 or ENSG00000227471" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "1.1.1.-" @@ -271474,7 +271474,7 @@ - MAM03176c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000111716 or ENSG00000134333 or ENSG00000166796 or ENSG00000166800 or ENSG00000166816 or ENSG00000171989" + - gene_reaction_rule: "ENSG00000111716 or ENSG00000134333 or ENSG00000166796 or ENSG00000166816 or ENSG00000171989" - rxnNotes: "https://www.springer.com/gp/book/9789400957800" - rxnFrom: "Recon3D" - eccodes: "1.1.1.27" @@ -306836,9 +306836,6 @@ - !!omap - id: "ENSG00000111224" - name: "PARP11" - - !!omap - - id: "ENSG00000111237" - - name: "VPS29" - !!omap - id: "ENSG00000111261" - name: "MANSC1" diff --git a/model/genes.tsv b/model/genes.tsv index 5ec73e81..c7c3f9e9 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -734,7 +734,6 @@ ENSG00000111077 "ENST00000379902;ENST00000314276;ENST00000549498;ENST00000551302 ENSG00000111144 "ENST00000228740;ENST00000537111;ENST00000552789;ENST00000553041;ENST00000413268;ENST00000548852;ENST00000547393;ENST00000548375;ENST00000547982;ENST00000552091" "ENSP00000228740;ENSP00000449958;ENSP00000395051;ENSP00000449340" P09960 LTA4H 4048 leukotriene A4 hydrolase "Nucleus;Cytosol" "SwissProt;CellAtlas" ENSG00000111181 "ENST00000359674;ENST00000545058;ENST00000424061;ENST00000536824;ENST00000542825;ENST00000535498;ENST00000544782;ENST00000538272;ENST00000540094;ENST00000538580;ENST00000536116;ENST00000537793;ENST00000535347;ENST00000537826;ENST00000538424;ENST00000397296;ENST00000684302" "ENSP00000352702;ENSP00000399136;ENSP00000444268;ENSP00000439351;ENSP00000446082;ENSP00000380464;ENSP00000508194" P48065 SLC6A12 6539 solute carrier family 6 member 12 BGT-1 Cell membrane DeepLoc2 ENSG00000111224 "ENST00000416739;ENST00000427057;ENST00000458162;ENST00000228820;ENST00000476985;ENST00000453942;ENST00000450737;ENST00000447133" "ENSP00000392392;ENSP00000397058;ENSP00000399665;ENSP00000228820;ENSP00000395062;ENSP00000387481;ENSP00000405385" Q9NR21 PARP11 57097 poly(ADP-ribose) polymerase family member 11 "ARTD11;C12orf6" "Nucleus;Cytosol" "SwissProt;CellAtlas" -ENSG00000111237 "ENST00000549578;ENST00000360579;ENST00000621131;ENST00000552130;ENST00000447578;ENST00000546588;ENST00000548539;ENST00000549970;ENST00000548259;ENST00000553128;ENST00000551655;ENST00000550267" "ENSP00000447058;ENSP00000353786;ENSP00000480853;ENSP00000449954;ENSP00000400048;ENSP00000449044;ENSP00000447634" Q9UBQ0 VPS29 51699 VPS29 retromer complex component "DC15;DC7;PEP11" Cytosol "SwissProt;CellAtlas" ENSG00000111261 "ENST00000535902;ENST00000396349;ENST00000545735;ENST00000543314" "ENSP00000438205;ENSP00000379638;ENSP00000445303;ENSP00000437624" Q9H8J5 MANSC1 54682 MANSC domain containing 1 "FLJ10298;LOH12CR3" Golgi apparatus CellAtlas ENSG00000111275 "ENST00000416293;ENST00000261733;ENST00000548536;ENST00000549106;ENST00000551450" "ENSP00000403349;ENSP00000261733;ENSP00000448179;ENSP00000474669" P05091 ALDH2 217 aldehyde dehydrogenase 2 family member Mitochondria SwissProt ENSG00000111339 "ENST00000228936;ENST00000430129;ENST00000544616;ENST00000420600" "ENSP00000228936;ENSP00000412735;ENSP00000442877;ENSP00000405689" Q93070 ART4 420 ADP-ribosyltransferase 4 (inactive) (Dombrock blood group) "ARTC4;CD297;DO;DOK1" Cytosol CellAtlas