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Open Access Highly Accessed Methodology article

Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion

Sepideh Babaei12, Marc Hulsman1, Marcel Reinders12* and Jeroen de Ridder12*

Author affiliations

1 Delft Bioinformatics Lab, Delft University of Technology, Delft, The Netherlands

2 , Netherlands Bioinformatics Centre, The Netherlands

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Citation and License

BMC Bioinformatics 2013, 14:29  doi:10.1186/1471-2105-14-29

Published: 23 January 2013



Delineating the molecular drivers of cancer, i.e. determining cancer genes and the pathways which they deregulate, is an important challenge in cancer research. In this study, we aim to identify pathways of frequently mutated genes by exploiting their network neighborhood encoded in the protein-protein interaction network. To this end, we introduce a multi-scale diffusion kernel and apply it to a large collection of murine retroviral insertional mutagenesis data. The diffusion strength plays the role of scale parameter, determining the size of the network neighborhood that is taken into account. As a result, in addition to detecting genes with frequent mutations in their genomic vicinity, we find genes that harbor frequent mutations in their interaction network context.


We identify densely connected components of known and putatively novel cancer genes and demonstrate that they are strongly enriched for cancer related pathways across the diffusion scales. Moreover, the mutations in the clusters exhibit a significant pattern of mutual exclusion, supporting the conjecture that such genes are functionally linked. Using multi-scale diffusion kernel, various infrequently mutated genes are found to harbor significant numbers of mutations in their interaction network neighborhood. Many of them are well-known cancer genes.


The results demonstrate the importance of defining recurrent mutations while taking into account the interaction network context. Importantly, the putative cancer genes and networks detected in this study are found to be significant at different diffusion scales, confirming the necessity of a multi-scale analysis.