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Table 2 Major output files of iCAGES

From: iCAGES: integrated CAncer GEnome Score for comprehensively prioritizing driver genes in personal cancer genomes

Category Column name Description Example
Mutation prioritization output Gene name HUGO name of the gene ARAF
Chromosome number Chromosome number of this mutation 1
Coordinate Genomic coordinate of the mutation 1234560
Reference allele Reference allele of this mutation C
Alternative allele Alternative allele of this mutation G
Mutation category Whether this mutation is a point coding mutation, point non-coding mutation, or structural variation Point coding mutation
Mutation context Genomic context of the mutation c.641C > G
Protein context Protein context of the mutation p.S214C
Score category If the mutation is a point coding mutation, then the category is the radial SVM score; if a point non-coding mutation, then Funseq2 score; if structural variation, then normalized CNV signal score Radial SVM
Driver mutation score Value of the corresponding score 0.932
Gene prioritization output Gene name HUGO name of the gene ARAF
Gene category Whether this gene belongs to the Cancer Gene Census, KEGG Cancer Pathway, or other categories KEGG cancer pathway
Maximum radial SVM score Maximum radial SVM score of all point coding mutations in the gene 0.932
Maximum FunSeq2 Score Maximum FunSeq2 score of all point non-coding mutations in the gene 0.000
Maximum normalized CNV Signal score Maximum normalized CNV signal score of all structural variations in the gene 0.000
Phenolyzer score Phenolyzer score of the gene 0.306
iCAGES gene score iCAGES gene score of the gene 0.484
Drug prioritization output Drug name Name of the drug SORAFENIB
Final target gene Mutated gene in the patient finally targeted by the drug ARAF
Direct target gene Mutated gene in the patient directly targeted by the drug ARAF
iCAGES gene score iCAGES gene score of the target gene 0.484
BioSystems normalized Relatedness probability BioSystems normalized relatedness probability between the direct target of the drug and the target gene 1.000
PubChem normalized drug active probability PubChem normalized drug active probability of this drug 1.000
iCAGES drug score iCAGES drug score of the drug 0.484
Tier Which tier this drug belongs to, whether it is FDA approved (tier 1), undergoing clinical trials (tier 2) or otherwise (tier 3). 1
Brand name Commercial brand name of this drug NEXAVAR
FDA approved subtype What cancer subtypes approved by FDA can this drug be applied to Hepatocellular carcinoma, renal cancer, thyroid cancer
Clinical trial name The name of the active clinical trials on this drug Sorafenib phase II study for Japanese anaplastic or medullary thyroid carcinoma patients
Clinical trial organization The organization for this clinical trial BAYER
Clinical trial phase Phase of this clinical trial 2
Clinical trial URL URL of this clinical trial http://clinicaltrials.gov/show/nct02114658