Lec0I-networks

Lec0I-networks - Biological Networks CMSC 423 / BISCI 648a...

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Unformatted text preview: Biological Networks CMSC 423 / BISCI 648a Suggested Reading Paper Lists: http://www.cs.umd.edu/class/fall2007/cmsc858l/ http://www.cs.umd.edu/class/fall2009/cmsc858l/papers.html Reviews: 1. Zhu, Gerstein, Snyder. Getting connected: analysis and principles of biological networks , Genes Dev 21:1010-1024, 2007. 2. Shoemaker and Panchenko. Deciphering Protein-Protein Interactions. Part I. Experimental Techniques and Databases , PLoS Comp. Biol. 3(3):e42, 2007. 3. Kelley, Sharan, Karp, Sittler, Root, Stockwell, Ideker. Conserved pathways within bacteria and yeast as revealed by global protein network alignment , Proc. Natl. Acad. Sci. USA 100:11394-11399, 2003. 4. Sharan, Ulitsky, Shamir. Network-based prediction of protein function , Mol. Syst. Biol. 3, 2007. 5. Milo, Shen-Orr, Itzkovitz, Kashtan, Chklovskii, Alon. Network motifs: simple building blocks of complex networks . Science 298:824-827, 2002. Types of Biological Networks Yeast transcription network Yeast Protein-Protein interaction network Yeast Phosphorylation network E. coli metabolic network Yeast SSL network Zhu et al, 2007. Transcription network, aka regulatory network: Transcription Factors = proteins that bind to DNA to activate or repress the nearby, downstream genes. gene regulates gene the regulated gene might also be a transcription factor leads to a directed graph Protein-Protein interaction network: Proteins physically interact Edge {A,B} A B Assumption of binary interactions is imperfect. Sometimes several proteins must bind simultaneously for there to be any interaction (could be modeled as a hyperedge) Metabolic network Proteins are enzymes. They label the edges and their substrates are the nodes. Valine, Leucine, and Isoleucine biosynthesis ( from KEGG ) Yeast (aka Saccharomyces cerevisiae) interaction network (Two-hybrid) GRID (http:// thebiogrid.org ) 8,742 edges 3113 nodes (= proteins) (out of ~6,000 genes) Protein Experimental Interaction Human interaction network (Two-hybrid) 6,434 edges 4,083 nodes (out of ~25,000 genes) Why proteins interact: A A B B C C D D E E Bring chains of enzymes together A B C Signal Transduction Form structures A B C Tethered Signal...
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This note was uploaded on 01/13/2012 for the course CMSC 423 taught by Professor Staff during the Fall '07 term at Maryland.

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Lec0I-networks - Biological Networks CMSC 423 / BISCI 648a...

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