From 8a855e87d7fb17e5a7b760da3038430f9550c5ce Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Sat, 7 Dec 2024 11:03:57 +0800 Subject: [PATCH 1/3] Fix: GPR curation for subsystems related with amino acid --- model/Human-GEM.yml | 21 +++++++++------------ model/genes.tsv | 1 - 2 files changed, 9 insertions(+), 13 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 7a41c271..278e3b90 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -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" @@ -80744,7 +80744,7 @@ - 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.-" @@ -85711,7 +85711,7 @@ - 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" @@ -86410,7 +86410,7 @@ - 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" @@ -86668,7 +86668,7 @@ - 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" @@ -86882,7 +86882,7 @@ - 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" @@ -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" @@ -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" @@ -218356,7 +218356,7 @@ - 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" @@ -311948,9 +311948,6 @@ - !!omap - id: "ENSG00000181555" - name: "SETD2" - - !!omap - - id: "ENSG00000181652" - - name: "ATG9B" - !!omap - id: "ENSG00000181788" - name: "SIAH2" diff --git a/model/genes.tsv b/model/genes.tsv index 763bde13..1178753a 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -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 From bc79aec5d1921ad51098a12fc2a0b80d02d7e86c Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Sat, 7 Dec 2024 03:19:20 +0000 Subject: [PATCH 2/3] chore: add macaw test result --- data/testResults/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index adfaae5b..c83a2491 100644 --- 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 #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. From f9d560dbf290e630a6801958f4d1b7f47d0184bb Mon Sep 17 00:00:00 2001 From: feiranl Date: Mon, 16 Dec 2024 11:44:51 +0000 Subject: [PATCH 3/3] chore: add macaw test result --- data/testResults/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 1e25d652..c83a2491 100644 --- 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 #937** (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.