From 3534582b31213b1b6df102a05fd8af340574a323 Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 23 Dec 2024 20:19:17 +0800 Subject: [PATCH 1/4] fix: GPR curation for Arg_Pro_Tyr_metabolism --- model/Human-GEM.yml | 31 ++++++++++++++----------------- model/genes.tsv | 1 - 2 files changed, 14 insertions(+), 18 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 78429615..89c79c40 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -69497,7 +69497,7 @@ - MAM02039m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000142920" + - gene_reaction_rule: "" - rxnFrom: "HMRdatabase" - eccodes: "4.1.1.19" - references: "PMID:10800966;PMID:14738999" @@ -70338,7 +70338,7 @@ - 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" @@ -70356,7 +70356,7 @@ - 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" @@ -70603,7 +70603,7 @@ - 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" @@ -72872,7 +72872,7 @@ - MAM02152c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000117305" + - gene_reaction_rule: "" - rxnFrom: "HMRdatabase" - eccodes: "4.4.1.22" - subsystem: @@ -72927,7 +72927,7 @@ - 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" @@ -72948,7 +72948,7 @@ - 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" @@ -72969,7 +72969,7 @@ - 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" @@ -72988,7 +72988,7 @@ - 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" @@ -73150,7 +73150,7 @@ - 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: @@ -73291,7 +73291,7 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000077498" + - gene_reaction_rule: "" - rxnFrom: "HMRdatabase" - eccodes: "1.14.18.1" - subsystem: @@ -200810,7 +200810,7 @@ - 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" @@ -239964,7 +239964,7 @@ - MAM03564c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108" + - gene_reaction_rule: "" - rxnFrom: "Recon3D" - eccodes: "2.4.1.17" - references: "PMID:19116261" @@ -239982,7 +239982,7 @@ - MAM03563c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108" + - gene_reaction_rule: "" - rxnFrom: "Recon3D" - eccodes: "2.4.1.17" - references: "PMID:23683503" @@ -264773,9 +264773,6 @@ - !!omap - id: "ENSG00000142892" - name: "PIGK" - - !!omap - - id: "ENSG00000142920" - - name: "AZIN2" - !!omap - id: "ENSG00000142973" - name: "CYP4B1" diff --git a/model/genes.tsv b/model/genes.tsv index 26405529..86cfc73a 100644 --- a/model/genes.tsv +++ b/model/genes.tsv @@ -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" From 17d7270f10792d1461c3bfa6798e5abaa49d9813 Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Mon, 23 Dec 2024 12:32:20 +0000 Subject: [PATCH 2/4] 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 7d79c2be..4869565a 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -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. From 7f6ee40b5bfbb5aa33453b43442abff4ee2f657f Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Mon, 23 Dec 2024 21:44:33 +0800 Subject: [PATCH 3/4] Fix: remove empty "gene_reaction_rule" --- model/Human-GEM.yml | 5 ----- 1 file changed, 5 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index 89c79c40..655afc41 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -69497,7 +69497,6 @@ - MAM02039m: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "" - rxnFrom: "HMRdatabase" - eccodes: "4.1.1.19" - references: "PMID:10800966;PMID:14738999" @@ -72872,7 +72871,6 @@ - MAM02152c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "" - rxnFrom: "HMRdatabase" - eccodes: "4.4.1.22" - subsystem: @@ -73291,7 +73289,6 @@ - MAM02630c: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "" - rxnFrom: "HMRdatabase" - eccodes: "1.14.18.1" - subsystem: @@ -239964,7 +239961,6 @@ - MAM03564c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "" - rxnFrom: "Recon3D" - eccodes: "2.4.1.17" - references: "PMID:19116261" @@ -239982,7 +239978,6 @@ - MAM03563c: 1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "" - rxnFrom: "Recon3D" - eccodes: "2.4.1.17" - references: "PMID:23683503" From a70a9df2a9b03d388f63ba8f1f7ccf7ed664e507 Mon Sep 17 00:00:00 2001 From: feiranl Date: Thu, 9 Jan 2025 00:05:10 +0100 Subject: [PATCH 4/4] chore: add gene essentiality test result --- data/testResults/README.md | 2 +- data/testResults/gene-essential.csv | 12 ++++++------ 2 files changed, 7 insertions(+), 7 deletions(-) diff --git a/data/testResults/README.md b/data/testResults/README.md index 15c5048a..2a415d36 100644 --- a/data/testResults/README.md +++ b/data/testResults/README.md @@ -5,7 +5,7 @@ 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 #941** (MACAW) -- **PR #883** (gene essentiality) +- **PR #941** (gene essentiality) The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request. diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv index 90a498c1..c918efe0 100644 --- a/data/testResults/gene-essential.csv +++ b/data/testResults/gene-essential.csv @@ -1,7 +1,7 @@ cellLine,TP,TN,FP,FN,accuracy,sensitivity,specificity,F1,MCC -DLD1,37,2165,62,277,0.8666,0.1178,0.9722,0.1792,0.1531 -GBM,34,2147,65,294,0.8587,0.1037,0.9706,0.1593,0.1287 -HCT116,46,2189,57,305,0.8606,0.1311,0.9746,0.2026,0.1851 -HELA,31,2246,72,249,0.8764,0.1107,0.9689,0.1619,0.1266 -RPE1,15,2186,84,255,0.8665,0.05556,0.963,0.0813,0.02954 -all,7,2386,96,109,0.9211,0.06034,0.9613,0.06393,0.02293 +DLD1,50,2147,85,272,0.8602,0.1553,0.9619,0.2188,0.1739 +GBM,57,2138,78,280,0.8598,0.1691,0.9648,0.2415,0.2026 +HCT116,71,2179,70,289,0.8624,0.1972,0.9689,0.2834,0.2534 +HELA,35,2219,106,251,0.8633,0.1224,0.9544,0.1639,0.1061 +RPE1,21,2163,114,255,0.8555,0.07609,0.9499,0.1022,0.0361 +all,8,2357,133,113,0.9058,0.06612,0.9466,0.06107,0.01181