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SHORTCUT BASED GRAPH COARSENING FOR PROTEIN INTERACTION NETWORK VISUALIZATION

ZHONG, LI
http://rave.ohiolink.edu/etdc/view?acc_num=ucin997457452

Abstract Details

2001, MS, University of Cincinnati, Engineering : Computer Science.
Protein-protein interactions play important role in various biological processes. These interactions inside an organism constitute a complex network. A global view of this network is very useful in providing molecular and genetic scientists with a reference guide to aid detailed exploration of the functions of proteins. In this thesis, we build up a network, named as CID(Connected Interaction Database), whose links are defined as the interactions between proteins in S.Cerevisiae. The topological properties of this CID network have been studied and compared with another network called CSD(Connected Similarity Database), in which a link denotes either an physical interaction or functional similarity. The topological results imply that both CID and CSD possess the "small world" structure, where shortcuts play important role in shortening the path length between different clusters. We propose a graph coarsening algorithm based on these shortcuts and cut nodes to identify clusters presented in these network and generate a simplified "backbone" structure of CID and CSD. Studies on the "functional" distribution inside some clusters demonstrate that proteins with similar function (in broad sense as referring to both "cellular role" and "biological function") are more likely to be clustered together. Using the combination of physical interaction and sequence similarity data, we correctly predicted functional categories for 82.67% among the 3,116 characterized proteins with at least one partner (the proteins that have connections with the protein under study) of known function and functional categories for 907 previously uncharacterized proteins have been predicted.
Dr. Yizong Cheng (Advisor)
78 p.
Computer Science
graph coarsening; graph visualization; small world; protein network

Recommended Citations

Citations

  • ZHONG, L. (2001). SHORTCUT BASED GRAPH COARSENING FOR PROTEIN INTERACTION NETWORK VISUALIZATION [Master's thesis, University of Cincinnati]. OhioLINK Electronic Theses and Dissertations Center. http://rave.ohiolink.edu/etdc/view?acc_num=ucin997457452

    APA Style (7th edition)

  • ZHONG, LI. SHORTCUT BASED GRAPH COARSENING FOR PROTEIN INTERACTION NETWORK VISUALIZATION. 2001. University of Cincinnati, Master's thesis. OhioLINK Electronic Theses and Dissertations Center, http://rave.ohiolink.edu/etdc/view?acc_num=ucin997457452.

    MLA Style (8th edition)

  • ZHONG, LI. "SHORTCUT BASED GRAPH COARSENING FOR PROTEIN INTERACTION NETWORK VISUALIZATION." Master's thesis, University of Cincinnati, 2001. http://rave.ohiolink.edu/etdc/view?acc_num=ucin997457452

    Chicago Manual of Style (17th edition)

ucin997457452
648
© 2001, all rights reserved.
This open access ETD is published by University of Cincinnati and OhioLINK.