title: The interactome as a tree--an attempt to visualize the protein-protein interaction network in yeast.
abstract: The refinement and high-throughput of protein interaction detection methods offer us a protein-protein interaction network in yeast. The challenge coming along with the network is to find better ways to make it accessible for biological investigation. Visualization would be helpful for extraction of meaningful biological information from the network. However, traditional ways of visualizing the network are unsuitable because of the large number of proteins. Here, we provide a simple but information-rich approach for visualization which integrates topological and biological information. In our method, the topological information such as quasi-cliques or spoke-like modules of the network is extracted into a clustering tree, where biological information spanning from protein functional annotation to expression profile correlations can be annotated onto the representation of it. We have developed a software named PINC based on our approach. Compared with previous clustering methods, our clustering method ADJW performs well both in retaining a meaningful image of the protein interaction network as well as in enriching the image with biological information, therefore is more suitable in visualization of the network.
authors.affiliation: Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, Peoples Republic of China.
authors.forename: Hongchao
authors.initials: H
authors.lastname: Lu
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Haifeng
authors.initials: H
authors.lastname: Liu
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Jingfen
authors.initials: J
authors.lastname: Zhang
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Lun
authors.initials: L
authors.lastname: Cai
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhao
authors.forename: Shiwei
authors.initials: S
authors.lastname: Sun
authors.forename: Jingyi
authors.initials: J
authors.lastname: Xu
authors.forename: Dongbo
authors.initials: D
authors.lastname: Bu
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D003196:Computer Graphics; D025941:Protein Interaction Mapping; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D012984:Software
chemical_list: D029701:Saccharomyces cerevisiae Proteins