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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