Integrative biomarker discovery for breast cancer metastasis from gene expression and protein interaction data using error-tolerant pattern mining

Rohit Gupta, Smita Agrawal, Navneet Rao, Ze Tian, Rui Kuang, Vipin Kumar

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Scopus citations

Abstract

Biomarker discovery for complex diseases is a challenging problem. Most of the existing approaches identify individual genes as disease markers, thereby missing the interactions among genes. Moreover, often only single biological data source is used to discover biomarkers. These factors account for the discovery of inconsistent biomark-ers. In this paper, we propose a novel error-tolerant pattern mining approach for integrated analysis of gene expression and protein interaction data. This integrated approach incorporates constraints from protein interaction network and efficiently discovers patterns (groups of genes) in a bottom-up fashion from the gene-expression data. We call these patterns active sub-network biomarkers. To illustrate the efficacy of our proposed approach, we used four breast cancer gene expression data sets and a human protein interaction network and showed that active sub-network biomark-ers are more biologically plausible and genes discovered are more reproducible across studies. Finally, through pathway analysis, we also showed a substantial enrichment for known cancer genes and hence were able to generate relevant hypotheses for understanding the molecular mechanisms of breast cancer metastasis.

Original languageEnglish (US)
Title of host publication2nd International Conference on Bioinformatics and Computational Biology 2010, BICoB 2010
Pages171-176
Number of pages6
StatePublished - Dec 1 2010
Event2nd International Conference on Bioinformatics and Computational Biology 2010, BICoB 2010 - Honolulu, HI, United States
Duration: Mar 24 2010Mar 26 2010

Publication series

Name2nd International Conference on Bioinformatics and Computational Biology 2010, BICoB 2010

Other

Other2nd International Conference on Bioinformatics and Computational Biology 2010, BICoB 2010
Country/TerritoryUnited States
CityHonolulu, HI
Period3/24/103/26/10

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