Network-based integration of multi-omics data for prioritizing cancer genes

Dimitrakopoulos, Christos and Kumar Hindupur, Sravanth and Häfliger, Luca and Behr, Jonas and Montazeri, Hesam and Hall, Michael N. and Beerenwinkel, Niko. (2018) Network-based integration of multi-omics data for prioritizing cancer genes. Bioinformatics . pp. 1-7.

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Several molecular events are known to be cancer-related, including genomic aberrations, hypermethylation of gene promoter regions, and differential expression of microRNAs. These aberration events are very heterogeneous across tumors and it is poorly understood how they affect the molecular makeup of the cell, including the transcriptome and proteome. Protein interaction networks can help decode the functional relationship between aberration events and changes in gene and protein expression.; We developed NetICS (Network-based Integration of Multi-omics Data), a new graph diffusion-based method for prioritizing cancer genes by integrating diverse molecular data types on a directed functional interaction network. NetICS prioritizes genes by their mediator effect, defined as the proximity of the gene to upstream aberration events and to downstream differentially expressed genes and proteins in an interaction network. Genes are prioritized for individual samples separately and integrated using a robust rank aggregation technique. NetICS provides a comprehensive computational framework that can aid in explaining the heterogeneity of aberration events by their functional convergence to common differentially expressed genes and proteins. We demonstrate NetICS' competitive performance in predicting known cancer genes and in generating robust gene lists using TCGA data from five cancer types.; NetICS is available at https://github.com/cbg-ethz/netics.; niko.beerenwinkel@bsse.ethz.ch.; Supplementary data are available at Bioinformatics online.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Growth & Development > Biochemistry (Hall)
UniBasel Contributors:Hall, Michael N.
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Oxford University Press
Note:Publication type according to Uni Basel Research Database: Journal article
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Last Modified:17 May 2018 10:26
Deposited On:23 Mar 2018 15:41

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