Functional and genetic analysis of the colon cancer network

Frank Emmert-Streib, Ricardo de Matos Simoes, Galina Glazko, Simon McDade, Benjamin Haibe-Kains, Andreas Holzinger, Matthias Dehmer, Frederick Charles Campbell

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Abstract

Cancer is a complex disease that has proven to be difficult to understand on the single-gene level. For this reason a functional elucidation needs to take interactions among genes on a systems-level into account. In this study, we infer a colon cancer network from a large-scale gene expression data set by using the method BC3Net. We provide a structural and a functional analysis of this network and also connect its molecular interaction structure with the chromosomal locations of the genes enabling the definition of cis- and trans-interactions. Furthermore, we investigate the interaction of genes that can be found in close neighborhoods on the chromosomes to gain insight into regulatory mechanisms. To our knowledge this is the first study analyzing the genome-scale colon cancer network.

Original languageEnglish
Number of pages15
JournalBMC Bioinformatics
Volume15
Issue numberSuppl 6
DOIs
Publication statusPublished - 16 May 2014

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Bibliographical note

This MS has identified interactive molecular networks that associate with colorectal cancer

Keywords

  • Colonic Neoplasms
  • Computational Biology
  • Gene Expression Profiling
  • Gene Regulatory Networks
  • Humans
  • Proteins

Cite this

Emmert-Streib, F., de Matos Simoes, R., Glazko, G., McDade, S., Haibe-Kains, B., Holzinger, A., Dehmer, M., & Campbell, F. C. (2014). Functional and genetic analysis of the colon cancer network. BMC Bioinformatics, 15 (Suppl 6). https://doi.org/10.1186/1471-2105-15-S6-S6