Main areas. Cancer

OncodriveFM

Oncodrive-FM is an gene-centric approach to uncover driver genes or gene modules. It computes a metric of functional impact using three well-known methods (SIFT, PolyPhen2 and MutationAssessor) and assesses how the functional impact of variants found in a gene across several tumor samples deviates from a null distribution. It is thus based on the assumption that any bias towards the accumulation of variants with high functional impact is an indication of positive selection and can thus be used to detect candidate driver genes or gene modules.

More information.

####Citing

• Gonzalez-Perez A and Lopez-Bigas N. 2012. Functional impact bias reveals cancer drivers. Nucleic Acids Res., 10.1093/nar/gks743.

OncodriveClust

OncodriveCLUST is a gene-centric method aimed to identify genes whose mutations are biased towards a large spatial clustering (that is, a region of the gene). This method is designed to exploit the feature that mutations in cancer genes, especially oncogenes, often cluster in particular positions of the protein. The method consider this as a sign that mutations in these regions change the function of these proteins in a manner that provides an adaptive advantage to cancer cells and consequently are positively selected during clonal evolution of tumours, and this property can thus be used to nominate novel candidate driver genes.

More information.

####Citing

• Tamborero D, Gonzalez-Perez A and Lopez-Bigas N. OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics. 2013; doi: 10.1093/bioinformatics/btt395s