Cancer gene collections

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Reliable cancer gene collections are useful in cancer research. Here I list several such resources.

These sets can be devided into two categories: mutation- or data-based, and literature- or knowledge-based.

Mutation-based

COSMIC Cancer Gene Census (CGC)

The Catalogue of Somatic Mutations in Cancer (COSMIC) Cancer Gene Census (CGC) is an expert-curated description of the genes driving human cancer. The figure following shows the curation process.

It comprises two tiers.

  • To classify as Tier 1, a gene must possess a documented and reproducible activity relevant to cancer, along with evidence of mutations in cancer that change the activity of the gene product in a way that promotes oncogenic transformation.
  • Included in Tier 2 are genes with mutation patterns typical for oncogenes or TSGs but that have less well-established functional evidence in the scientific literature. Similarly, genes with strong published evidence for a function in cancer but unclear mutation patterns or genes known to be dysregulated solely by epigenetic means (for example, by changes to promoter methylation) are also included in Tier 2.

Comments

Lever et al. 2019

The Cancer Gene Census (CGC) uses data from the Catalogue of Somatic Mutations in Cancer (COSMIC) to list known oncogenes and tumor suppressors.

20/20 rule

The authors used mutation patterns to classify genes of the COSMIC database into oncogenes and tumor supressor genes.

  • To be classified as an oncogene, we simply require that >20% of the recorded mutations in the gene are at recurrent positions and are missense.
  • To be classified as a tumor suppressor gene, we analogously require that >20% of the recorded mutations in the gene are inactivating.

Network of Cancer Genes (NCG)

Genes in NCG were collected from 275 publications, including two sources of known cancer genes and 273 cancer sequencing screens of more than 100 cancer types from 34,905 cancer donors and multiple primary sites.

Comments

Lever et al. 2019

The Network of Cancer Genes builds upon the CGC and integrates a wide variety of additional contextual data, such as the frequency of mutations.

IntOGen

IntOGen-mutations is a Web platform used to identify cancer drivers across tumor types and to present the results of the systematic analysis of most currently available large data sets of tumor somatic mutations.

Comments

Lever et al. 2019

IntOGen uses data from large-scale sequencing projects (for example, the Cancer Genome Atlas (TCGA)) to collate the importance of cancer genes.

Candidate Cancer Gene Database (CCGD)

The Candidate Cancer Gene Database (CCGD) was developed to disseminate the results of transposon-based forward genetic screens in mice that identify candidate cancer genes. The purpose of the database is to allow cancer researchers to quickly determine whether or not a gene, or list of genes, has been identified as a potential cancer driver in a forward genetic screen in mice.

Literature-based

Lever et al. 2019

All manually curated databases face the overwhelming curation burden of expert curator time and costs necessary to stay up-to-date.

CancerMine

CancerMine a literature-mined database of drivers, oncogenes and tumor suppressors in cancer. The authors first manually annotated the drivers, oncogenes and tumor suppressors discussed in 1,500 sentences as training data. Then they trained a logistic regression classifier on word frequencies and semantic features. To lower the number of false positives, a high threshold was uded, resulting relatively high precision and low recall (average precision of 85.6% and recall of 29.4% across the three gene role types).

CancerMine contains substantially more cancer gene associations than other resources but has poor overlap with CGC and IntOGen. The authors explained this as “gene associations in the CGC and IntOGen are not mentioned in the literature”.

ONGene

ONGene is a database for oncogenes. The authors manually curated abstracts from PubMed (Dec 25th, 2015) and collected 803 human oncogenes (698 protein-coding genes and 105 non-coding genes.)

This database is simple and has high utility.

Comments

Lever et al. 2019

ONGene and TSGene list oncogenes and tumor suppressors but do not associate them with specific cancer types.

TSGene

TSGene is a database for tumor suppressor genes. The authors manually curated abstracts from PubMed (25 April 2015) and collected 1217 human TSGs (1018 protein-coding genes and 199 non-coding genes.)

Comments

Lever et al. 2019

ONGene and TSGene list oncogenes and tumor suppressors but do not associate them with specific cancer types.

Clinical Interpretation of Variants in Cancer (CIViC)

CIViC is an expert-crowdsourced knowledgebase for Clinical Interpretation of Variants in Cancer describing the therapeutic, prognostic, diagnostic and predisposing relevance of inherited and somatic variants of all types.

Change log

  • 20190602: create the note.
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