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

Christos Dimitrakopoulos1,2, Sravanth Kumar Hindupur3, Luca Häfliger1

  • 1Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland.

Bioinformatics (Oxford, England)
|March 17, 2018
PubMed
Abstract

Insights

NetICS prioritizes cancer genes by integrating multi-omics data on a functional network. This method explains tumor heterogeneity by linking aberration events to gene expression changes.

Area of Science:

  • Computational biology
  • Genomics
  • Cancer research

Background:

  • Cancer is characterized by molecular aberrations like genomic changes, promoter hypermethylation, and microRNA dysregulation.
  • Tumor heterogeneity complicates understanding how these events impact cellular transcriptome and proteome.
  • Protein interaction networks offer a way to link aberration events to gene and protein expression changes.

Purpose of the Study:

  • To develop a computational method for prioritizing cancer genes by integrating diverse molecular data.
  • To explain tumor heterogeneity by identifying functional convergence of aberration events.

Main Methods:

  • Developed NetICS (Network-based Integration of Multi-omics Data), a graph diffusion-based method.
  • Integrated multi-omics data onto a directed functional interaction network.
  • Prioritized genes based on mediator effect (proximity to aberrations and differential expression) and aggregated ranks.

Main Results:

  • NetICS successfully prioritized cancer genes by integrating multi-omics data.
  • The method demonstrated competitive performance in predicting known cancer genes.
  • Generated robust gene lists from TCGA data across five cancer types, aiding in explaining heterogeneity.

Conclusions:

  • NetICS provides a framework for understanding cancer gene function and tumor heterogeneity.
  • The integration of multi-omics data through network analysis is crucial for cancer research.
  • NetICS aids in identifying key genes driving cancer development and progression.

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