diff --git a/data/testResults/gene-essential.csv b/data/testResults/gene-essential.csv index 21f17d16..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 -DLD1,39,2155,63,279,0.8651,0.1226,0.9716,0.1857,0.1588 -GBM,35,2134,67,299,0.8556,0.1048,0.9696,0.1606,0.128 -HCT116,49,2179,57,306,0.8599,0.138,0.9745,0.2126,0.1954 -HELA,32,2237,74,250,0.875,0.1135,0.968,0.1649,0.1281 -RPE1,15,2175,87,258,0.8639,0.05495,0.9615,0.08,0.026 -all,7,2375,99,112,0.9186,0.05882,0.96,0.06222,0.01988 +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 diff --git a/model/Human-GEM.yml b/model/Human-GEM.yml index c85322e5..fe801ce2 100644 --- a/model/Human-GEM.yml +++ b/model/Human-GEM.yml @@ -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 ENSG00000196177" - rxnFrom: "HMRdatabase" - eccodes: - "1.3.99.3" @@ -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 ENSG00000196177" - rxnFrom: "HMRdatabase" - eccodes: "1.3.99.3" - references: "PMID:13295225;PMID:3597357" @@ -71033,7 +71033,7 @@ - MAM02468m: -1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000122971 or ENSG00000196177" + - gene_reaction_rule: "ENSG00000151498 or ENSG00000122971 or ENSG00000196177" - rxnFrom: "HMRdatabase" - eccodes: - "1.3.8.5" @@ -71122,7 +71122,7 @@ - MAM02999m: 1 - lower_bound: -1000 - upper_bound: 1000 - - gene_reaction_rule: "ENSG00000122971 or ENSG00000196177" + - gene_reaction_rule: "ENSG00000151498 or ENSG00000122971 or ENSG00000196177" - rxnFrom: "HMRdatabase" - eccodes: - "1.3.8.5" @@ -96075,7 +96075,7 @@ - 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" @@ -96315,7 +96315,7 @@ - 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" @@ -105177,13 +105177,14 @@ - 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 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 @@ -105245,13 +105246,14 @@ - 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 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 @@ -200147,7 +200149,7 @@ - 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" @@ -203271,7 +203273,7 @@ - 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"