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Uppalapati, PraneethNetwork Mining Approach to Cancer Biomarker Discovery
Master of Science, The Ohio State University, 2010, Computer Science and Engineering

With the rapid development of high throughput gene expression profiling technology, molecule profiling has become a powerful tool to characterize disease subtypes and discover gene signatures. Most existing gene signature discovery methods apply statistical methods to select genes whose expression values can differentiate different subject groups. However, a drawback of these approaches is that the selected genes are not functionally related and hence cannot reveal biological mechanism behind the difference in the patient groups.

Gene co-expression network analysis can be used to mine functionally related sets of genes that can be marked as potential biomarkers through survival analysis. We present an efficient heuristic algorithm EigenCut that exploits the properties of gene co-expression networks to mine functionally related and dense modules of genes. We apply this method to brain tumor (Glioblastoma Multiforme) study to obtain functionally related clusters. If functional groups of genes with predictive power on patient prognosis can be identified, insights on the mechanisms related to metastasis in GBM can be obtained and better therapeutical plan can be developed. We predicted potential biomarkers by dividing the patients into two groups based on their expression profiles over the genes in the clusters and comparing their survival outcome through survival analysis. We obtained 12 potential biomarkers with log-rank test p-values less than 0.01.


Kun Huang, PhD (Committee Chair); Raghu Machiraju, PhD (Committee Member)


Bioinformatics; Computer Science


Biomarker; Gene co-expression networks; Glioblastoma Multiforme; Network mining; Biological networks