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Remove peroxisomal genes from mitochondrial ACAD reactions #943

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Remove peroxisomal genes from mitochondrial ACAD reactions #943

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0c64152
fix: remove peroxisomal genes from mitochondrial acyl-CoA dehydrogena…
Devlin-Moyer Dec 23, 2024
61f560c
chore: add macaw test result
Devlin-Moyer Dec 23, 2024
6f98208
fix: adds ACAD11 to GPRs of MAR03107 and MAR03111 to ensure it is sti…
Devlin-Moyer Dec 23, 2024
b1e5f2b
Merge branch 'fix/acad_gprs' of https://github.com/SysBioChalmers/Hum…
Devlin-Moyer Dec 23, 2024
dca5683
chore: add gene essentiality test result
Devlin-Moyer Dec 24, 2024
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4 changes: 2 additions & 2 deletions data/testResults/README.md
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Expand Up @@ -4,8 +4,8 @@ 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 #830** (MACAW)
- **PR #883** (gene essentiality)
- **PR #943** (MACAW)
- **PR #943** (gene essentiality)

The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request.

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12 changes: 6 additions & 6 deletions data/testResults/gene-essential.csv
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Original file line number Diff line number Diff line change
@@ -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
18 changes: 10 additions & 8 deletions model/Human-GEM.yml
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Expand Up @@ -62692,7 +62692,7 @@
- MAM02774m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117054 or ENSG00000122971 or ENSG00000151498 or ENSG00000177646 or ENSG00000196177 or ENSG00000240303"
- gene_reaction_rule: "ENSG00000122971 or ENSG00000151498 or ENSG00000196177"
- rxnFrom: "HMRdatabase"
- eccodes:
- "1.3.99.3"
Expand Down Expand Up @@ -63045,7 +63045,7 @@
- MAM01803m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000117054 or ENSG00000122971 or ENSG00000151498 or ENSG00000177646 or ENSG00000196177 or ENSG00000240303"
- gene_reaction_rule: "ENSG00000122971 or ENSG00000151498 or ENSG00000196177"
- rxnFrom: "HMRdatabase"
- eccodes: "1.3.99.3"
- references: "PMID:13295225;PMID:3597357"
Expand Down Expand Up @@ -96078,7 +96078,7 @@
- MAM02630m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000087008 or ENSG00000161533"
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000177646"
- rxnFrom: "HMRdatabase"
- eccodes: "1.3.3.6"
- references: "PMID:12054595"
Expand Down Expand Up @@ -96318,7 +96318,7 @@
- MAM02630m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000087008 or ENSG00000161533"
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000177646"
- rxnFrom: "HMRdatabase"
- eccodes: "1.3.3.6"
- references: "PMID:11368003;PMID:9862787"
Expand Down Expand Up @@ -105180,13 +105180,14 @@
- MAM01803m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646"
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646 or ENSG00000240303"
- rxnFrom: "HMRdatabase"
- eccodes:
- "1.3.8.7"
- "1.3.8.8"
- "1.3.8.9"
- "1.3.99.-"
- references: "PMID:21237683"
- subsystem:
- "Beta oxidation of even-chain fatty acids (mitochondrial)"
- confidence_score: 0
Expand Down Expand Up @@ -105248,13 +105249,14 @@
- MAM01803m: 1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646"
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361 or ENSG00000117054 or ENSG00000177646 or ENSG00000240303"
- rxnFrom: "HMRdatabase"
- eccodes:
- "1.3.8.7"
- "1.3.8.8"
- "1.3.8.9"
- "1.3.99.-"
- references: "PMID:21237683"
- subsystem:
- "Beta oxidation of even-chain fatty acids (mitochondrial)"
- confidence_score: 0
Expand Down Expand Up @@ -200344,7 +200346,7 @@
- MAM03333m: -1
- lower_bound: -1000
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000115361 or ENSG00000117054 or ENSG00000196177"
- gene_reaction_rule: "ENSG00000115361"
- rxnFrom: "Recon3D"
- eccodes: "1.3.99.3"
- references: "PMID:1047780;PMID:11135616;PMID:8973539"
Expand Down Expand Up @@ -203468,7 +203470,7 @@
- MAM03352m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000161533"
- gene_reaction_rule: "ENSG00000072778 or ENSG00000115361"
- rxnFrom: "Recon3D"
- eccodes: "1.3.3.6"
- references: "PMID:11356164;PMID:7775433"
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