de novo Generation, Visualization, and Analysis of Biological Networks using Cytoscape and Agilent Literature Search

Allan Kuchinsky

Agilent Technologies, Santa Clara, California, USA

Analyzing high-throughput experimental data in the context of biological processes can be a daunting task. For example, analysis of microarray data is useful only in identifying statistically significant gene expression changes, whereas identifying discriminatory pathways/networks of gene interactions from a set of significant molecules can provide critical information for understanding complex processes and identifying therapeutic targets from among the potentially large list of differentially expressed genes. I will present a systems-based method to analyze high-throughput data for studying complex diseases, based upon literature-based de novo network construction, supplemented by visualization techniques for examining generated networks against experimental data.

Central to our approach are two software systems:

I will provide an in-depth look at Cytoscape and Agilent Literature Search and discusses their application in collaborative studies with researchers at the Stanford University School of Medicine in the area of cardiovascular disease.

Data keywords: gene expression, scientific text, unstructured data sources, increased resolution of data analysis

Cytoscape keywords: connectivity analysis, data overlay, multi-datapoint visualization (heatstrips)


J.Y. King, R. Ferrara, R. Tabibiazar, J.M. Spin, M.M. Chen, A. Kuchinsky, A. Vailaya, R.Kincaid, A. Tsalenko, D. Deng, A. Connolly, P. Zhang, E. Yang, C. Watt, Z.Yakhini, A. Ben-Dor, A.Adler, L. Bruhn, P. Tsao, T. Quertermous, E.A. Ashley, “Pathway analysis of coronary atherosclerosis”, Physiol. Genomics Jun 07, 2005 0: 1012005

A. Vailaya, P. Bluvas, R. Kincaid, Allan Kuchinsky, M. L. Creech, A. Adler: “An architecture for biological information extraction and representation”. Bioinformatics 21(4): 430-438 (2005)

AtheroSclerosisDemo (last edited 2009-02-12 01:03:14 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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