423f11-netalign

423f11-netalign - Network Alignment 858L Types of...

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Unformatted text preview: Network Alignment 858L 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) interacti on 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) Terms & Questions Interolog = A B h(A) h(B) Species 1 Species 2 homologous Are there conserved pathways? What is the minimum set of pathways required for life? Can we compare networks to develop an evolutionary distance? Aligning Networks ❖ Let G 1 = ( V 1 , E 1 ) , G 2 , ... G k be graphs, each giving noisy experimental estimations of interactions between proteins in organisms 1 ,.., k. ❖ If G i = ( V i , E i ) , we also have a function: that gives the sequence similarity between u and v . sim ( u , v ) : V i × V j → R G 1 G 2 Combining Sequence and Network Topology Conservation ⇒ Functional Importance ❖ If a structure has withstood millions of years of the randomizing process of mutations, then it likely has an...
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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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423f11-netalign - Network Alignment 858L Types of...

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