Fix: Pyrimidine_metabolism

SysBioChalmers · Dec 5, 2024 · 0afca1b · 0afca1b
1 parent 5e88b8a
commit 0afca1b
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Showing 2 changed files with 14 additions and 18 deletions.
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -73347,7 +73347,7 @@
           - MAM03130c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
+      - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.4.6"
@@ -73365,7 +73365,7 @@
           - MAM01623c: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
+      - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.4.6"
@@ -73383,7 +73383,7 @@
           - MAM01623m: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000143156 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
+      - gene_reaction_rule: "ENSG00000103024 or ENSG00000103202 or ENSG00000172113 or ENSG00000239672 or ENSG00000243678"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.4.6"
@@ -73757,7 +73757,7 @@
           - MAM03114c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000154269 or ENSG00000183828 or ENSG00000197594"
+      - gene_reaction_rule: "ENSG00000183828 or ENSG00000197594"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.6.1.8;3.6.1.9;3.6.1.45"
@@ -73775,7 +73775,7 @@
           - MAM02751c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000185013"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -73793,7 +73793,7 @@
           - MAM02751e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -73812,7 +73812,7 @@
           - MAM02039c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000116199 or ENSG00000141560 or ENSG00000162408 or ENSG00000167363 or ENSG00000172456"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.-"
@@ -73911,7 +73911,7 @@
           - MAM03130e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125877"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.6.1.19"
@@ -73966,7 +73966,7 @@
           - MAM02040c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000092964 or ENSG00000147647"
+      - gene_reaction_rule: "ENSG00000147647"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.5.2.2"
@@ -74041,7 +74041,7 @@
           - MAM02996m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000185013 or ENSG00000205309"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5;3.1.3.35"
@@ -74077,7 +74077,7 @@
           - MAM02751c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013 or ENSG00000205309"
+      - gene_reaction_rule: "ENSG00000014257 or ENSG00000076685 or ENSG00000116981 or ENSG00000122643 or ENSG00000125458 or ENSG00000135318 or ENSG00000141698 or ENSG00000146587 or ENSG00000185013"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.1.3.5"
@@ -74277,7 +74277,7 @@
           - MAM02759m: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000125877 or ENSG00000128951"
+      - gene_reaction_rule: "ENSG00000128951"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.6.1.23;3.6.1.19"
@@ -74332,7 +74332,7 @@
           - MAM02039c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000130717 or ENSG00000143179 or ENSG00000198276"
+      - gene_reaction_rule: "ENSG00000143179 or ENSG00000198276"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.48"
@@ -74558,7 +74558,7 @@
           - MAM02039c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000167900"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "2.7.1.21"
@@ -305852,9 +305852,6 @@
     - !!omap
       - id: "ENSG00000092621"
       - name: "PHGDH"
-    - !!omap
-      - id: "ENSG00000092964"
-      - name: "DPYSL2"
     - !!omap
       - id: "ENSG00000093000"
       - name: "NUP50"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -391,7 +391,6 @@ ENSG00000092148	"ENST00000554882;ENST00000399332;ENST00000555843;ENST00000611816
 ENSG00000092295	"ENST00000206765;ENST00000544573;ENST00000559669;ENST00000559136;ENST00000558074;ENST00000560443;ENST00000560478;ENST00000560226;ENST00000561067"	"ENSP00000206765;ENSP00000439446;ENSP00000453701;ENSP00000453337;ENSP00000453840;ENSP00000452822;ENSP00000453234;ENSP00000454070;ENSP00000452690"	P22735	TGM1	7051	transglutaminase 1	"ICR2;LI;LI1;TGASE;TGK"	Cytosol	DeepLoc2
 ENSG00000092529	"ENST00000349748;ENST00000397163;ENST00000357568;ENST00000638141;ENST00000673705;ENST00000673658;ENST00000673813;ENST00000397200;ENST00000569827;ENST00000673646;ENST00000567071;ENST00000673854;ENST00000674093;ENST00000569136;ENST00000673936;ENST00000673890;ENST00000674149;ENST00000673771;ENST00000337571;ENST00000673743;ENST00000673939;ENST00000674146;ENST00000674119;ENST00000674064;ENST00000673692;ENST00000565173;ENST00000674052;ENST00000561817;ENST00000674018;ENST00000397204;ENST00000673886;ENST00000674139;ENST00000673851;ENST00000673839;ENST00000673978;ENST00000673987;ENST00000673928;ENST00000674041;ENST00000565559;ENST00000673750;ENST00000674011;ENST00000674135;ENST00000674012;ENST00000565274;ENST00000674140;ENST00000564503;ENST00000673774;ENST00000673950;ENST00000466222;ENST00000673687;ENST00000674027;ENST00000674130;ENST00000562199;ENST00000673893;ENST00000673684;ENST00000568153;ENST00000567817;ENST00000356316;ENST00000318023"	"ENSP00000183936;ENSP00000380349;ENSP00000350181;ENSP00000501021;ENSP00000380384;ENSP00000454379;ENSP00000501007;ENSP00000456607;ENSP00000501303;ENSP00000455254;ENSP00000501189;ENSP00000501293;ENSP00000501112;ENSP00000501023;ENSP00000336840;ENSP00000500989;ENSP00000501129;ENSP00000501175;ENSP00000501217;ENSP00000501138;ENSP00000501057;ENSP00000456575;ENSP00000501271;ENSP00000380387;ENSP00000501155;ENSP00000501054;ENSP00000501142;ENSP00000501188;ENSP00000500976;ENSP00000501231;ENSP00000501099;ENSP00000500956;ENSP00000457878;ENSP00000501173;ENSP00000501171;ENSP00000501178;ENSP00000457759;ENSP00000457898;ENSP00000501034;ENSP00000500987;ENSP00000454937;ENSP00000456514;ENSP00000348667;ENSP00000326281"	P20807	CAPN3	825	calpain 3	"CANP3;LGMD2;LGMD2A;nCL-1;p94"	"Cytosol;Nucleus"	SwissProt
 ENSG00000092621	"ENST00000641597;ENST00000493622;ENST00000641720;ENST00000642041;ENST00000641947;ENST00000641213;ENST00000641074;ENST00000496756;ENST00000641115;ENST00000642021;ENST00000641491;ENST00000369409;ENST00000641023;ENST00000641513;ENST00000641573;ENST00000641587;ENST00000641570;ENST00000641891;ENST00000641375;ENST00000462324;ENST00000641371;ENST00000641272;ENST00000641247;ENST00000641756;ENST00000641711;ENST00000641927;ENST00000641314;ENST00000369407;ENST00000641811;ENST00000641847;ENST00000641455;ENST00000469443;ENST00000641939;ENST00000482968"	"ENSP00000493382;ENSP00000493433;ENSP00000492948;ENSP00000493415;ENSP00000492994;ENSP00000493079;ENSP00000493446;ENSP00000493264;ENSP00000493187;ENSP00000358417;ENSP00000493175;ENSP00000493398;ENSP00000493453;ENSP00000493213;ENSP00000493288;ENSP00000493089;ENSP00000493305;ENSP00000493432;ENSP00000492955;ENSP00000493147;ENSP00000493296"	O43175	PHGDH	26227	phosphoglycerate dehydrogenase	"PDG;PGDH;SERA"	"Cytosol;Nucleus"	CellAtlas
-ENSG00000092964	"ENST00000521913;ENST00000493789;ENST00000311151;ENST00000523027;ENST00000523690;ENST00000523093;ENST00000521983;ENST00000474808"	"ENSP00000427985;ENSP00000427954;ENSP00000309539;ENSP00000431117"	Q16555	DPYSL2	1808	dihydropyrimidinase like 2	"CRMP2;DHPRP2;DRP-2;DRP2"	Cytosol	"SwissProt;CellAtlas"
 ENSG00000093000	"ENST00000347635;ENST00000407019;ENST00000424634;ENST00000417702;ENST00000497960;ENST00000461437;ENST00000434760;ENST00000430547;ENST00000484186;ENST00000445721;ENST00000493456;ENST00000396096;ENST00000461194;ENST00000432340;ENST00000419387;ENST00000422489;ENST00000486184;ENST00000491860;ENST00000469163"	"ENSP00000345895;ENSP00000385555;ENSP00000415062;ENSP00000394450;ENSP00000388426;ENSP00000397960;ENSP00000398297;ENSP00000379403;ENSP00000400465;ENSP00000391987;ENSP00000416264"	Q9UKX7	NUP50	10762	nucleoporin 50	NPAP60L	Nucleus	"SwissProt;CellAtlas"
 ENSG00000093010	"ENST00000676678;ENST00000403184;ENST00000361682;ENST00000403710;ENST00000407537;ENST00000467943;ENST00000678868;ENST00000678769;ENST00000428707;ENST00000412786;ENST00000207636;ENST00000406520;ENST00000678255;ENST00000449653;ENST00000677397;ENST00000678240;ENST00000677675;ENST00000493893;ENST00000678945;ENST00000677564;ENST00000677470"	"ENSP00000503719;ENSP00000383966;ENSP00000354511;ENSP00000385917;ENSP00000384654;ENSP00000503583;ENSP00000503289;ENSP00000387695;ENSP00000403958;ENSP00000207636;ENSP00000385150;ENSP00000504402;ENSP00000416778;ENSP00000503422"	P21964	COMT	1312	catechol-O-methyltransferase		"Endoplasmic reticulum;Cytosol"	"SwissProt;CellAtlas"
 ENSG00000093072	"ENST00000399837;ENST00000399839;ENST00000330232;ENST00000262607;ENST00000648668;ENST00000648061;ENST00000449907;ENST00000649540;ENST00000649915;ENST00000469063;ENST00000480276;ENST00000650635;ENST00000648343;ENST00000543038;ENST00000441548;ENST00000649310;ENST00000649746;ENST00000610390"	"ENSP00000382731;ENSP00000382733;ENSP00000332871;ENSP00000262607;ENSP00000496894;ENSP00000406443;ENSP00000497469;ENSP00000497681;ENSP00000442482;ENSP00000392078;ENSP00000496839;ENSP00000497913;ENSP00000483418"	Q9NZK5	ADA2	51816	adenosine deaminase 2	"ADGF;CECR1;IDGFL"	Lysosome	DeepLoc2