Fix: GPR curation for Androgen metabolism and Prostaglandin biosynthe…

…sis (#935) * Fix: GPR curation for Androgen metabolism and Prostaglandin biosynthesis * chore: add macaw test result * chore: add gene essentiality test result --------- Co-authored-by: JHL-452b <[email protected]> Co-authored-by: feiranl <[email protected]> Co-authored-by: feiranl <[email protected]> Co-authored-by: Eduard Kerkhoven <[email protected]>
SysBioChalmers · Dec 17, 2024 · 5af4173 · 5af4173
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diff --git 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 #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.
+The test results shown here were obtained by the GitHub Actions run in **PR #935** (MACAW) and **PR #935** (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.

diff --git 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
-DLD1,36,2185,59,279,0.8679,0.1143,0.9737,0.1756,0.1529
-GBM,34,2165,61,298,0.8597,0.1024,0.9726,0.1593,0.1333
-HCT116,46,2207,53,309,0.8616,0.1296,0.9765,0.2026,0.1905
-HELA,30,2263,69,254,0.8765,0.1056,0.9704,0.1567,0.124
-RPE1,14,2204,81,259,0.8671,0.05128,0.9646,0.07609,0.02585
-all,7,2408,92,109,0.9232,0.06034,0.9632,0.06512,0.0254
+DLD1,36,2183,59,279,0.8678,0.1143,0.9737,0.1756,0.1529
+GBM,34,2163,61,298,0.8595,0.1024,0.9726,0.1593,0.1333
+HCT116,46,2205,53,309,0.8615,0.1296,0.9765,0.2026,0.1904
+HELA,30,2262,69,253,0.8768,0.106,0.9704,0.1571,0.1244
+RPE1,14,2202,81,259,0.867,0.05128,0.9645,0.07609,0.0258
+all,7,2406,92,109,0.9231,0.06034,0.9632,0.06512,0.02537
diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml
@@ -123722,7 +123722,7 @@
           - MAM02630c: -1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000148795 or ENSG00000197580"
+      - gene_reaction_rule: "ENSG00000148795"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.14.99.-"
@@ -123743,7 +123743,7 @@
           - MAM02630r: -1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000148795 or ENSG00000197580"
+      - gene_reaction_rule: "ENSG00000148795"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.14.99.-"
@@ -123895,7 +123895,7 @@
           - MAM02969c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000025423 or ENSG00000086696 or ENSG00000108786 or ENSG00000130948 or ENSG00000132196 or ENSG00000149084 or ENSG00000196139 or ENSG00000198189 or ENSG00000204228"
+      - gene_reaction_rule: "ENSG00000025423 or ENSG00000086696 or ENSG00000108786 or ENSG00000130948 or ENSG00000132196 or ENSG00000196139 or ENSG00000198189 or ENSG00000204228"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.62;1.1.1.64"
@@ -123914,7 +123914,7 @@
           - MAM02969r: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000025423 or ENSG00000086696 or ENSG00000108786 or ENSG00000130948 or ENSG00000132196 or ENSG00000149084 or ENSG00000196139 or ENSG00000198189 or ENSG00000204228"
+      - gene_reaction_rule: "ENSG00000025423 or ENSG00000108786 or ENSG00000130948 or ENSG00000132196 or ENSG00000149084 or ENSG00000196139 or ENSG00000198189"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.62;1.1.1.64"
@@ -137858,7 +137858,7 @@
           - MAM02786c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000163684 or ENSG00000244486"
+      - gene_reaction_rule: "ENSG00000244486"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.-"
@@ -137926,7 +137926,7 @@
           - MAM02794c: 1
       - lower_bound: 0
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000196139"
+      - gene_reaction_rule: ""
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "1.1.1.188"
@@ -138855,7 +138855,7 @@
           - MAM02785c: 1
       - lower_bound: -1000
       - upper_bound: 1000
-      - gene_reaction_rule: "ENSG00000163684 or ENSG00000244486"
+      - gene_reaction_rule: "ENSG00000244486"
       - rxnNotes: ""
       - rxnFrom: "HMRdatabase"
       - eccodes: "4.2.1.-"