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Table 1 Twenty-six features derived from molecular and systems-level properties of genes and used to predict cancer drivers in sysSVM2. Molecular properties describe gene alterations in individual cancer samples. Systems-level properties are global gene properties (see also Additional file 2: Table S1)

From: Pan-cancer detection of driver genes at the single-patient resolution

Category

Property

Feature

Type

Molecular

Gene mutation

Mutational load (n)

Continuous

Non-truncating damaging mutations (n)

Continuous

Truncating mutations (n)

Continuous

Hotspot mutations (n)

Continuous

Gene copy number

Gene copy number (n)

Continuous

Gene is amplified

Binary

Gene is deleted

Binary

Systems-level

Gene duplication

Gene is duplicated

Binary

Gene is an ohnolog

Binary

Gene essentiality

Cell lines in which gene is essential (%)

Continuous

Gene is essential

Binary

Gene expression

Tissues expressing gene (n)

Continuous

Gene is expressed in 0 tissues

Binary

Gene is expressed in 7 ≤ tissues ≤ 36

Binary

Protein expression

Tissues expressing protein (n)

Continuous

Protein is expressed in ≥ 41 tissues

Binary

Protein-protein interaction network (PPIN)

PPIN degree

Continuous

Protein is a PPIN hub

Binary

PPIN betweenness

Continuous

PPIN clustering coefficient

Continuous

Protein complexes

Complexes the protein is part of (n)

Continuous

miRNA interactions

miRNAs targeting the gene (n)

Continuous

Gene evolutionary origin

Pre-metazoan origin

Binary

Metazoan origin

Binary

Vertebrate origin

Binary

Post-vertebrate origin

Binary

  1. PPIN protein-protein interaction network, miRNA micro RNA