fix-GPR curation for Galactose, Fructose and mannose metabolism

SysBioChalmers · Oct 28, 2024 · c7e9f61 · c7e9f61
1 parent 760b376
commit c7e9f61
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Showing 2 changed files with 12 additions and 20 deletions.
diff --git 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"
@@ -223353,7 +223353,7 @@
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "2.7.1.3"
-      - references: "PMID:33715524"
+      - references: "PMID:33715524;PMID:2469615;PMID:19158351"
       - subsystem:
           - "Galactose metabolism"
       - confidence_score: 0
@@ -307346,9 +307346,6 @@
     - !!omap
       - id: "ENSG00000116771"
       - name: "AGMAT"
-    - !!omap
-      - id: "ENSG00000116783"
-      - name: "TNNI3K"
     - !!omap
       - id: "ENSG00000116791"
       - name: "CRYZ"
@@ -313091,9 +313088,6 @@
     - !!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
@@ -886,7 +886,6 @@ 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
@@ -2784,7 +2783,6 @@ 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"