Merge pull request #933 from SysBioChalmers/Fix-Starch_and_sucrose_me…

…tabolism Fix: GPR curation for starch and sucrose metabolism
SysBioChalmers · Dec 16, 2024 · 1ecf471 · 1ecf471
2 parents 12fa860 + 30975e8
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diff --git a/data/testResults/README.md b/data/testResults/README.md
@@ -2,7 +2,7 @@
 
 The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/macaw) `dead_end_test` and `duplicate_test` tests, and from cell-line specific gene essentiality prediction based on the [Hart _et al._ (2015)](https://doi.org/10.1016/j.cell.2015.11.015) dataset.
 
-The test results shown here were obtained by the GitHub Actions run in **PR #936** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
+The test results shown here were obtained by the GitHub Actions run in **PR #933** (MACAW) and **PR #675** (gene essentiality), and will be updated by any subsequent PR. Summary results are shown as a comment in the corresponding PR.
 
 ### MACAW: `dead_end_test`
 Looks for metabolites in Human-GEM that can only be produced by all reactions they participate in or only consumed, then identifies all reactions that are prevented from sustaining steady-state fluxes because of each of these dead-end metabolites. The simplest case of a dead-end metabolite is one that only participates in a single reaction. Also flags all reversible reactions that can only carry fluxes in a single direction because one of their metabolites can either only be consumed or only be produced by all other reactions it participates in.

diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -68303,7 +68303,7 @@
           - MAM02450e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000092529 or ENSG00000171298 or ENSG00000214013 or ENSG00000257335"
+      - gene_reaction_rule: "ENSG00000171298 or ENSG00000214013 or ENSG00000257335"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.20"
@@ -68340,7 +68340,7 @@
           - MAM03039e: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000118094 or ENSG00000142102"
+      - gene_reaction_rule: "ENSG00000118094"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.28"
@@ -68500,7 +68500,7 @@
           - MAM02448c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68572,7 +68572,7 @@
           - MAM02447c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68608,7 +68608,7 @@
           - MAM02449c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68644,7 +68644,7 @@
           - MAM02451c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68680,7 +68680,7 @@
           - MAM02452c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68770,7 +68770,7 @@
           - MAM02452c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -68787,7 +68787,7 @@
           - MAM02450c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000120563 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "3.2.1.1"
@@ -218065,7 +218065,7 @@
           - MAM03622e: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "(ENSG00000021488 and ENSG00000138079) or ENSG00000168003 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
+      - gene_reaction_rule: "ENSG00000168003 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480"
       - rxnNotes: ""
       - rxnFrom: "Recon3D"
       - eccodes: "3.2.1.1"
@@ -305846,9 +305846,6 @@
     - !!omap
       - id: "ENSG00000092295"
       - name: "TGM1"
-    - !!omap
-      - id: "ENSG00000092529"
-      - name: "CAPN3"
     - !!omap
       - id: "ENSG00000092621"
       - name: "PHGDH"

diff --git a/model/genes.tsv b/model/genes.tsv
@@ -389,7 +389,6 @@ ENSG00000092068	"ENST00000339733;ENST00000316902;ENST00000397310;ENST00000422941
 ENSG00000092098	"ENST00000560875;ENST00000559308;ENST00000558634;ENST00000557878;ENST00000559533;ENST00000557991;ENST00000559438;ENST00000560071;ENST00000559275;ENST00000324103;ENST00000559882;ENST00000559260;ENST00000560342;ENST00000558907;ENST00000560787;ENST00000559583;ENST00000491351;ENST00000559071;ENST00000560754;ENST00000558452;ENST00000559449;ENST00000483895;ENST00000559719;ENST00000559491;ENST00000560631"	"ENSP00000454032;ENSP00000453471;ENSP00000454048;ENSP00000453423;ENSP00000453948;ENSP00000453574;ENSP00000315112;ENSP00000453645;ENSP00000453601;ENSP00000452972;ENSP00000499015;ENSP00000453595;ENSP00000454140;ENSP00000453672;ENSP00000452820"	Q96EP0	RNF31	55072	ring finger protein 31	"FLJ10111;FLJ23501;HOIP;Paul;ZIBRA"	Cytosol	"SwissProt;CellAtlas"
 ENSG00000092148	"ENST00000554882;ENST00000399332;ENST00000555843;ENST00000611816;ENST00000553700;ENST00000556281;ENST00000557695;ENST00000555311;ENST00000553957;ENST00000557321;ENST00000554027;ENST00000555915;ENST00000556004;ENST00000557369;ENST00000554850;ENST00000556224;ENST00000554471;ENST00000553616;ENST00000556474"	"ENSP00000451260;ENSP00000382269;ENSP00000484981;ENSP00000450697;ENSP00000451860;ENSP00000450920;ENSP00000452233;ENSP00000452015;ENSP00000479695"	Q9ULT8	HECTD1	25831	HECT domain E3 ubiquitin protein ligase 1	KIAA1131	Nucleus	CellAtlas
 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"