Dear All,

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Departmental Colloquium
Friday, March 13, 2009
1:00 p.m.–3:00 p.m.
Department Conference Room

Identification of molecular biomarkers by analyzing “omics” data 
using integrative systems biology strategy 

Dr. Youping Deng 
Senior Scientist, bioinformatics team leader 
the Specpro Inc, Vicksburg, Mississippi
E-mail: [log in to unmask]

“Omics” data include genomics, transcriptomics, proteomics and metabolomics data etc. As we know, “omics” data are exploding at an extremely fast pace. How to analyze these data is a critical issue. My lab has developed various methods for dealing with “omics” data analysis. I will give one example how I identify toxic biomarkers using integrative systems biology strategy.    

The munitions constituents (MCs) 2,4-DNT, 2,6-DNT, TNT and its degradation products, 4A-DNT and 2A-DNT can be toxic at high doses, however, their mechanism of toxicity is unclear. Here we describe the use of gene expression profiles and network modeling to identify biomarkers and understand the mechanisms of toxicity of these compounds. We used a total of 200 microarrays for the analysis. While each chemical induced a distinctive expression pattern, a common set of genes was affected by all chemicals. These genes were used to build a gene network, using both data from literature and microarray data. The resulting network was mainly involved in the Nrf2-mediated oxidative stress response, xenobiotic metabolism signaling and metabolism of xenobiotics by Cytochrome P450. Analysis of biological functions suggests that these genes are strongly associated with hepatic disease. We also constructed specific gene networks for each chemical, and found that they all strongly affected the Nrf2-mediated oxidative stress response pathway although the targeted genes for each compound were different.  Novel Nrf2 downstream target genes were further characterized using a couple of network inference algorithms.   Overall, our results indicate that a genomics and systems biology strategy can help to understand the common and specific mechanisms of toxicity of DNT, TNT and their derivatives. If time allows, I may talk more examples. 
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Dr. Youping Deng is a senior scientist, bioinformatics team leader in the Specpro Inc, Vicksburg, which is a contract company to serve the US Environmental Research Laboratory, in the Engineer Research and Development Center (ERDC) of the US Army Corps of Engineers. He is also adjunct faculty in the Department of Biological Sciences, University of Southern Mississippi as well as Associate Director of Bioinformatics, Mississippi Functional Genomics Network.  Before taking the current position, he was a tenure track assistant professor at the University of Southern Mississippi. Between 2002 and 2004, he was a research assistant professor and bioinformatics specialist, and established a Bioinformatics Center of Kansas State University, where he led a group to serve the whole university. He has published nearly 100 peer-reviewed papers.

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thanks!

yanqing zhang