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Fix: GPR curation for subsystems related with amino acid #936

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merged 4 commits into from
Dec 16, 2024
Merged

Fix: GPR curation for subsystems related with amino acid #936

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8a855e8
Fix: GPR curation for subsystems related with amino acid
JHL-452b Dec 7, 2024
bc79aec
chore: add macaw test result
JHL-452b Dec 7, 2024
9bcaa1d
Merge branch 'develop' into Fix-Subsystems_relate_to_amino_acid
feiranl Dec 16, 2024
f9d560d
chore: add macaw test result
feiranl Dec 16, 2024
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2 changes: 1 addition & 1 deletion data/testResults/README.md
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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 #913** (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 #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.

### 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.
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21 changes: 9 additions & 12 deletions model/Human-GEM.yml
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Expand Up @@ -77405,7 +77405,7 @@
- MAM02943m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000134333"
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.1.16"
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- MAM03124c: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000006695 or ENSG00000054267 or ENSG00000117682 or ENSG00000120942 or ENSG00000183665"
- gene_reaction_rule: "ENSG00000054267 or ENSG00000117682 or ENSG00000120942 or ENSG00000183665"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.5.1.-"
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- MAM02555c: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000181652 or ENSG00000184470 or ENSG00000197763 or ENSG00000198431"
- gene_reaction_rule: "ENSG00000184470 or ENSG00000197763 or ENSG00000198431"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.8.1.9"
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- MAM02041e: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000116157 or ENSG00000117450 or ENSG00000117592 or ENSG00000126432 or ENSG00000164294 or ENSG00000165672 or ENSG00000167468 or ENSG00000167815 or ENSG00000176153 or ENSG00000198704 or ENSG00000211445 or ENSG00000224586 or ENSG00000233276"
- gene_reaction_rule: "ENSG00000116157 or ENSG00000117450 or ENSG00000117592 or ENSG00000126432 or ENSG00000164294 or ENSG00000167468 or ENSG00000167815 or ENSG00000176153 or ENSG00000198704 or ENSG00000211445 or ENSG00000224586 or ENSG00000233276"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "1.11.1.9;1.11.1.15"
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- MAM02039c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000128683 or ENSG00000136750"
- gene_reaction_rule: "ENSG00000136750"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "4.1.1.11;4.1.1.15"
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- MAM02885c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000138801 or ENSG00000198682"
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "2.7.7.4"
Expand Down Expand Up @@ -88067,7 +88067,7 @@
- MAM02527c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000111261 or ENSG00000133048 or ENSG00000133063 or ENSG00000134216"
- gene_reaction_rule: "ENSG00000111261 or ENSG00000133063 or ENSG00000134216"
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "3.2.1.14"
Expand Down Expand Up @@ -93247,7 +93247,7 @@
- MAM03135c: 28
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000165996 or ENSG00000206527"
- gene_reaction_rule: ""
- rxnNotes: ""
- rxnFrom: "HMRdatabase"
- eccodes: "4.2.1.134"
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- MAM02553m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000111275 or ENSG00000137124 or ENSG00000159423"
- gene_reaction_rule: "ENSG00000111275 or ENSG00000137124"
- rxnNotes: ""
- rxnFrom: "Recon3D"
- eccodes: "1.5.1.12"
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- !!omap
- id: "ENSG00000181555"
- name: "SETD2"
- !!omap
- id: "ENSG00000181652"
- name: "ATG9B"
- !!omap
- id: "ENSG00000181788"
- name: "SIAH2"
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1 change: 0 additions & 1 deletion model/genes.tsv
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Expand Up @@ -2407,7 +2407,6 @@ ENSG00000181192 "ENST00000263035;ENST00000437298;ENST00000465617;ENST00000415935
ENSG00000181222 "ENST00000674977;ENST00000617998;ENST00000572844;ENST00000576952;ENST00000575547;ENST00000576114;ENST00000576718;ENST00000574158;ENST00000573603;ENST00000576553" ENSP00000502190 A0A6Q8PGB0 POLR2A 5430 RNA polymerase II subunit A "POLR2;POLRA;RPB1" "Cytosol;Nucleus" CellAtlas
ENSG00000181523 "ENST00000575484;ENST00000571156;ENST00000572257;ENST00000326317;ENST00000575282;ENST00000573150;ENST00000576856;ENST00000570923;ENST00000576941;ENST00000574505;ENST00000572208;ENST00000571051;ENST00000576707;ENST00000570427;ENST00000571675;ENST00000575188;ENST00000571075" "ENSP00000461827;ENSP00000314606;ENSP00000459280;ENSP00000460720;ENSP00000458200;ENSP00000461160;ENSP00000459708;ENSP00000461128;ENSP00000459765" P51688 SGSH 6448 N-sulfoglucosamine sulfohydrolase "HSS;MPS3A;SFMD" Lysosome SwissProt
ENSG00000181555 "ENST00000431180;ENST00000330022;ENST00000409792;ENST00000445387;ENST00000479832;ENST00000492397;ENST00000638947;ENST00000484689;ENST00000412450" "ENSP00000388349;ENSP00000332415;ENSP00000386759;ENSP00000411901;ENSP00000491413;ENSP00000416401" Q9BYW2 SETD2 29072 SET domain containing 2, histone lysine methyltransferase "FLJ23184;HIF-1;HYPB;KIAA1732;KMT3A" "Nucleus;Cytosol" "SwissProt;CellAtlas"
ENSG00000181652 "ENST00000498521;ENST00000605952;ENST00000639579;ENST00000617967;ENST00000404733;ENST00000476282;ENST00000471797;ENST00000611177;ENST00000469530;ENST00000473409;ENST00000473134;ENST00000466157" "ENSP00000475737;ENSP00000491504;ENSP00000479879" Q674R7 ATG9B 285973 autophagy related 9B "APG9L2;FLJ14885;NOS3AS;SONE" Cytosol SwissProt
ENSG00000181788 "ENST00000312960;ENST00000482706;ENST00000472885" "ENSP00000322457;ENSP00000417619" O43255 SIAH2 6478 siah E3 ubiquitin protein ligase 2 "Nucleus;Cytosol" "SwissProt;CellAtlas"
ENSG00000181789 "ENST00000314797;ENST00000513965;ENST00000515725;ENST00000504350;ENST00000509208;ENST00000504547;ENST00000513410;ENST00000509889;ENST00000514478;ENST00000512034" "ENSP00000325002;ENSP00000426457;ENSP00000422478;ENSP00000420916" Q9Y678 COPG1 22820 COPI coat complex subunit gamma 1 COPG "Golgi apparatus;Nucleus;Cytosol" "SwissProt;CellAtlas"
ENSG00000181804 "ENST00000316549;ENST00000483124;ENST00000474727;ENST00000474151;ENST00000498717" "ENSP00000320246;ENSP00000419090;ENSP00000418627" Q8IVB4 SLC9A9 285195 solute carrier family 9 member A9 "FLJ35613;NHE9" "Cell membrane;Lysosome" DeepLoc2
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