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Home | Seminars and Symposia | Past seminars/symposia: Friday, April 20, 2007

Protein Network Comparative Genomics

by

Trey Ideker
Department of Bioengineering
University of California, San Diego

Friday, April 20, 2007
12:00 Lunch
12:15 Seminar

402 Walter Library

Cells respond to toxic agents through the complex interplay of a variety of different signaling and regulatory pathways. Although the complete structure of these pathways has not yet been elucidated, protein interaction mapping projects provide the raw materials for mapping them at large-scale. We describe one such mapping project, involving systematic screens for transcriptional interactions that mediate the response to DNA alkylating agents. We also describe methods for mining these networks to model the effects of single and double genetic perturbations on the system-wide genotoxic response. These methods uniformly rely on the principle of network alignment and comparison — that is, the pathways of interest are efficiently mapped by comparing protein networks between toxic and non-toxic conditions, between genetic and physical maps, and between species.

Relevant articles and links:

Workman, CT., Mak, HC., McCuine, S., Tagne, JB., Agarwal, M., Ozier, O., Begley, TJ., Samson, LD., Ideker, T., “A Systems Approach to Mapping DNA Damage Response Pathways.” Science. 312 (5776):1054-1059 (2006).

Yeang, C.H., Mak, H.C., McCuine, S., Workman, C., Jaakkola, T., and Ideker, T., “Validation and refinement of gene regulatory pathways on a network of physical interactions.” Genome Biology 6(7): R62 (2005).

Kelley, R. and Ideker, T., “Systematic interpretation of genetic interactions using protein networks.” Nature Biotechnology 23(5):561-566 (2005).

http://www.cytoscape.org/

http://www.pathblast.org/