From 96a7288f91dc8f50bacce1a44aed5b14e609960a Mon Sep 17 00:00:00 2001 From: Jiahao Luo <67491919+JHL-452b@users.noreply.github.com> Date: Wed, 6 Nov 2024 15:40:33 +0800 Subject: [PATCH 1/2] fix-GPR_curation_for_Serotonin and melatonin biosynthesis and Keratan sulfate biosynthesis --- model/Human-GEM.yml | 64 ++++++++++++++++++++++----------------------- 1 file changed, 32 insertions(+), 32 deletions(-) diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index e9484f6b..e6937b9a 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -141463,7 +141463,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141501,7 +141501,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141520,7 +141520,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141558,7 +141558,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141577,7 +141577,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141615,7 +141615,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141634,7 +141634,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141672,7 +141672,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141691,7 +141691,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141729,7 +141729,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141748,7 +141748,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141786,7 +141786,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141805,7 +141805,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141843,7 +141843,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141862,7 +141862,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141900,7 +141900,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141919,7 +141919,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -141957,7 +141957,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -141976,7 +141976,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -142014,7 +142014,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142033,7 +142033,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -142071,7 +142071,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142185,7 +142185,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142223,7 +142223,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142242,7 +142242,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -142280,7 +142280,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142394,7 +142394,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142432,7 +142432,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142451,7 +142451,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -142489,7 +142489,7 @@ - MAM03111g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000175711 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" + - gene_reaction_rule: "ENSG00000156966 or ENSG00000170340 or ENSG00000174684 or ENSG00000176383 or ENSG00000177191 or ENSG00000179913" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "" @@ -142508,7 +142508,7 @@ - MAM02682g: -1 - lower_bound: 0 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196" + - gene_reaction_rule: "ENSG00000140835 or ENSG00000175040 or ENSG00000183196" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" @@ -156497,7 +156497,7 @@ - MAM02949c: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000070614 or ENSG00000111962 or ENSG00000115526 or ENSG00000124302 or ENSG00000130540 or ENSG00000135702 or ENSG00000136720 or ENSG00000138653 or ENSG00000140835 or ENSG00000147119 or ENSG00000153936 or ENSG00000154080 or ENSG00000154252 or ENSG00000164100 or ENSG00000166507 or ENSG00000171004 or ENSG00000173597 or ENSG00000175040 or ENSG00000175229 or ENSG00000183196 or ENSG00000185352 or ENSG00000197093 or ENSG00000198075 or ENSG00000198203 or ENSG00000261052" + - gene_reaction_rule: "ENSG00000070614 or ENSG00000115526 or ENSG00000130540 or ENSG00000135702 or ENSG00000138653 or ENSG00000147119 or ENSG00000153936 or ENSG00000154080 or ENSG00000173597 or ENSG00000197093 or ENSG00000198203 or ENSG00000261052" - rxnNotes: "" - rxnFrom: "HMRdatabase" - eccodes: "2.8.2.-" From 55e4b21761f2ce8e5c2fc421f702779dd57bcfeb Mon Sep 17 00:00:00 2001 From: JHL-452b Date: Wed, 6 Nov 2024 08:13:12 +0000 Subject: [PATCH 2/2] 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 160c9df5..3ed4bf13 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 #882** (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 #907** (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.