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transformed Functional Impact score for Cancer transFIC

A method to transform functional impact scores taking into account the differences in basal tolerance to germline SNVs of genes that belong to different functional classes. This transformation allows to use the scores provided by well-known tools (e.g. SIFT, Polyphen2, MutationAssessor) to rank the functional impact of cancer somatic mutations. Mutations with greater transFIC are more likely to be cancer drivers. TransFIC takes as input the Functional Impact Score of a somatic mutation observed in cancer provided by one of the aforementioned tools. It then compares that score to the distribution of scores of germline SNVs observed in genes with similar functional annotations (for instance genes with the same molecular function as provided by the Gene Ontologies). The score is thus transformed using the Zscore formula. The result is that mutations in genes that are less tolerant to germline SNVs are amplified, while the scores of mutations on relatively tolerant genes are decreased.

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transFIC classification

transFIC specifications

Interface:
Web user interface
Computer skills:
Basic
Maintained:
Yes
Restrictions to use:
None
Stability:
Stable

transFIC support

Maintainer

  • Abel González-Pérez <>

Credits

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Publications

Institution(s)

Research Programme on Biomedical Informatics - GRIB Universitat Pompeu Fabra - UPF, Hospital del Mar Medical Research Institute - IMIM Parc de Recerca Biomèdica de Barcelona (PRBB), Barcelona, Spain

Funding source(s)

The Spanish Ministry of Science and Technology (grant number SAF2009-06954); the Spanish National Institute of Bioinformatics (INB)

Link to literature

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