Ph.D. Research Proposal - Meta-Scale Bioinformatics Analysis in Cancer and Metastasis
Date: September 21, 2009
Time: 10:00 AM
Location: Bossone Research Enterprise Center, Room: 709
Speaker(s):
Noor Dawany
Advisor: Aydin Tozeren, Ph.D
Details:
While cancer encompasses a large number of different malignancies, cancer cells are generally characterized by their uncontrolled growth and invasiveness. Global gene expression analysis of cancer and healthy tissues typically results in large numbers of genes (SAM genes) that are significantly altered in cancer. Such data, however, has been difficult to interpret due to the high level of variation of gene lists across laboratories and the small sample sizes used in individual studies. In this study, I have compiled microarray data from 67 labs, resulting in a database containing 979 healthy tissue samples and 1,608 cancer samples for 11 different tissue types. The primary cancers considered involved brain, breast, cervix, colon, kidney, liver, lung, ovary, PBMC, prostate and skin tissues. This integrated approach produced top 100 SAM genes that were highly statistically enriched with genes already associated with cancer research publications. Moreover, SAM gene lists obtained for eleven different tissue types were also enriched with bimodal and housekeeping genes in all tissues considered. List of SAM genes that appeared in at least four cancer types partially intersected KEGG's pathways in cancer with p = 4E-75. Gene lists provided in this study and their annotation using a priori knowledge from large collections of microarray data will be useful in biomarker development and drug discovery. Future work will concentrate on the involvement of protein kinases in cancer as well as establishing correspondence between cell lines and tissue cells in a similar meta-scale analysis.
Biosketch:
Directions:
The Bossone Research Enterprise Center is located at the corner of 32nd and Market Streets.
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