Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Fix: GPR curation for Arg_Pro_Tyr_metabolism #941

Merged
merged 6 commits into from
Jan 13, 2025
Merged

Fix: GPR curation for Arg_Pro_Tyr_metabolism #941

Show file tree
Hide file tree
Changes from 3 commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
3534582
fix: GPR curation for Arg_Pro_Tyr_metabolism
JHL-452b Dec 23, 2024
17d7270
chore: add macaw test result
JHL-452b Dec 23, 2024
7f6ee40
Fix: remove empty "gene_reaction_rule"
JHL-452b Dec 23, 2024
21580af
Merge branch 'develop' into Fix_Arg_Pro_Tyr_metabolism
feiranl Jan 8, 2025
a70a9df
chore: add gene essentiality test result
feiranl Jan 8, 2025
8ce6988
Merge branch 'develop' into Fix_Arg_Pro_Tyr_metabolism
feiranl Jan 13, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion data/testResults/README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,7 +4,7 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/

The test results shown here were obtained by the GitHub Actions run in:

- **PR #939** (MACAW)
- **PR #941** (MACAW)
- **PR #883** (gene essentiality)

The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request.
Expand Down
26 changes: 9 additions & 17 deletions model/Human-GEM.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -69497,7 +69497,6 @@
- MAM02039m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000142920"
- rxnFrom: "HMRdatabase"
edkerk marked this conversation as resolved.
Show resolved Hide resolved
- eccodes: "4.1.1.19"
- references: "PMID:10800966;PMID:14738999"
Expand Down Expand Up @@ -70338,7 +70337,7 @@
- MAM02921c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000064763 or ENSG00000118514 or ENSG00000197601"
- gene_reaction_rule: "ENSG00000197601"
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.1.-"
- references: "PMID:7040832;PMID:10047787"
Expand All @@ -70356,7 +70355,7 @@
- MAM02922c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000064763 or ENSG00000118514 or ENSG00000197601"
- gene_reaction_rule: "ENSG00000118514 or ENSG00000197601"
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.1.-"
- references: "PMID:7040832;PMID:10047787"
Expand Down Expand Up @@ -70603,7 +70602,7 @@
- MAM02925c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000064763 or ENSG00000118514 or ENSG00000197601"
- gene_reaction_rule: "ENSG00000118514 or ENSG00000197601"
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.1.-"
- references: "PMID:10047787;PMID:7040832"
Expand Down Expand Up @@ -72872,7 +72871,6 @@
- MAM02152c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117305"
- rxnFrom: "HMRdatabase"
- eccodes: "4.4.1.22"
- subsystem:
Expand Down Expand Up @@ -72927,7 +72925,7 @@
- MAM02720c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
- gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746"
- rxnFrom: "HMRdatabase"
- eccodes:
- "1.2.1.5"
Expand All @@ -72948,7 +72946,7 @@
- MAM02720m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
- gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746"
- rxnFrom: "HMRdatabase"
- eccodes:
- "1.2.1.5"
Expand All @@ -72969,7 +72967,7 @@
- MAM02720c: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
- gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746"
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.1.5"
- references: "PMID:17379813;PMID:18621017"
Expand All @@ -72988,7 +72986,7 @@
- MAM02720m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254"
- gene_reaction_rule: "ENSG00000006534 or ENSG00000108602 or ENSG00000132746"
- rxnFrom: "HMRdatabase"
- eccodes: "1.2.1.5"
- references: "PMID:17379813;PMID:18621017"
Expand Down Expand Up @@ -73150,7 +73148,7 @@
- MAM02553c: 1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144"
- gene_reaction_rule: "ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000197894 or ENSG00000248144"
- rxnFrom: "HMRdatabase"
- eccodes: "1.1.1.1"
- subsystem:
Expand Down Expand Up @@ -73291,7 +73289,6 @@
- MAM02630c: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000077498"
- rxnFrom: "HMRdatabase"
- eccodes: "1.14.18.1"
- subsystem:
Expand Down Expand Up @@ -200810,7 +200807,7 @@
- MAM02041l: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000005381 or ENSG00000117592"
- gene_reaction_rule: "ENSG00000005381"
- rxnFrom: "Recon3D"
- eccodes: "1.11.1.7"
- references: "PMID:9164836"
Expand Down Expand Up @@ -239964,7 +239961,6 @@
- MAM03564c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108"
- rxnFrom: "Recon3D"
- eccodes: "2.4.1.17"
- references: "PMID:19116261"
Expand All @@ -239982,7 +239978,6 @@
- MAM03563c: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108"
- rxnFrom: "Recon3D"
- eccodes: "2.4.1.17"
- references: "PMID:23683503"
Expand Down Expand Up @@ -264773,9 +264768,6 @@
- !!omap
- id: "ENSG00000142892"
- name: "PIGK"
- !!omap
- id: "ENSG00000142920"
- name: "AZIN2"
- !!omap
- id: "ENSG00000142973"
- name: "CYP4B1"
Expand Down
1 change: 0 additions & 1 deletion model/genes.tsv
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1471,7 +1471,6 @@
"ENSG00000142623" "ENST00000375471;ENST00000483501;ENST00000648847;ENST00000460293" "ENSP00000364620" "Q9ULC6" "PADI1" "29943" "peptidyl arginine deiminase 1" "HPAD10;PAD1;PDI;PDI1" "Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000142657" "ENST00000491493;ENST00000487775;ENST00000270776;ENST00000477958;ENST00000483936;ENST00000465632;ENST00000460189;ENST00000493288;ENST00000498356;ENST00000496718" "ENSP00000466358;ENSP00000270776;ENSP00000465311;ENSP00000466156;ENSP00000466574;ENSP00000467362" "P52209" "PGD" "5226" "phosphogluconate dehydrogenase" "" "Cytosol" "SwissProt;CellAtlas"
"ENSG00000142892" "ENST00000370812;ENST00000445065;ENST00000487906;ENST00000359130;ENST00000478391" "ENSP00000359848;ENSP00000388854;ENSP00000474518;ENSP00000352041" "Q92643" "PIGK" "10026" "phosphatidylinositol glycan anchor biosynthesis class K" "GPI8;hGPI8" "Endoplasmic reticulum" "SwissProt"
"ENSG00000142920" "ENST00000478635;ENST00000481886;ENST00000475935;ENST00000294517;ENST00000462920;ENST00000471119;ENST00000495135;ENST00000477570;ENST00000483027;ENST00000492420;ENST00000373443;ENST00000497710;ENST00000473089;ENST00000652171;ENST00000484656;ENST00000373440;ENST00000652381;ENST00000373441;ENST00000478204;ENST00000497280;ENST00000492521" "ENSP00000294517;ENSP00000362542;ENSP00000498229;ENSP00000362539;ENSP00000362540" "Q96A70" "AZIN2" "113451" "antizyme inhibitor 2" "ADC;KIAA1945;ODC-p;ODC1L;ODCp" "Endoplasmic reticulum;Golgi apparatus;Nucleus;Cytosol" "SwissProt;CellAtlas"
"ENSG00000142973" "ENST00000546128;ENST00000413093;ENST00000640628;ENST00000534708;ENST00000271153;ENST00000371923;ENST00000529715;ENST00000464439;ENST00000371919;ENST00000614163;ENST00000526297;ENST00000452782;ENST00000468637;ENST00000481248;ENST00000497005" "ENSP00000492115;ENSP00000433367;ENSP00000271153;ENSP00000360991;ENSP00000443212;ENSP00000433068;ENSP00000360987;ENSP00000484629;ENSP00000438995" "P13584" "CYP4B1" "1580" "cytochrome P450 family 4 subfamily B member 1" "" "Endoplasmic reticulum" "SwissProt"
"ENSG00000143036" "ENST00000446120;ENST00000271227;ENST00000527077;ENST00000529450;ENST00000467909;ENST00000422520;ENST00000532427;ENST00000475883;ENST00000530397;ENST00000532670" "ENSP00000389143;ENSP00000271227;ENSP00000433641;ENSP00000431836;ENSP00000432789;ENSP00000410832;ENSP00000436661;ENSP00000434457;ENSP00000432880" "Q8N4M1" "SLC44A3" "126969" "solute carrier family 44 member 3" "CTL3;MGC45474" "Cell membrane" "DeepLoc2"
"ENSG00000143149" "ENST00000354775;ENST00000463610;ENST00000491436;ENST00000461664;ENST00000471457" "ENSP00000346827" "P49189" "ALDH9A1" "223" "aldehyde dehydrogenase 9 family member A1" "ALDH4;ALDH7;ALDH9;E3" "Cytosol" "SwissProt;CellAtlas"
Expand Down
Loading