Browse > Article

Protein Interaction Network Visualization System Combined with Gene Ontology  

Choi, Yun-Kyu (한국과학기술원 정보통신공학과)
Kim, Seok (한국과학기술원 전산학과)
Yi, Gwan-Su (한국과학기술원 바이오 및 뇌공학과)
Park, Jin-Ah (한국과학기술원 전산학과)
Publication Information
Journal of KIISE:Computer Systems and Theory / v.36, no.2, 2009 , pp. 60-67 More about this Journal
Abstract
Analyzing protein-protein interactions(PPI) is an important task in bioinformatics as it can help in new drugs' discovery process. However, due to vast amount of PPI data and their complexity, efficient visualization of the data is still remained as a challenging problem. We have developed efficient and effective visualization system that integrates Gene Ontology(GO) and PPI network to provide better insights to scientists. To provide efficient data visualization, we have employed dynamic interactive graph drawing methods and context-based browsing strategy. In addition, quick and flexible cross-reference system between GO and PPI; LCA(Least Common Ancestor) finding for GO; and etc are supported as special features. In terms of interface, our visualization system provides two separate graphical windows side-by-side for GO graphs and PPI network, and also provides cross-reference functions between them.
Keywords
Protein-protein interaction; Gene Ontology; Dynamic Graph; Context-based browsing; Least Common Ancestor;
Citations & Related Records
Times Cited By KSCI : 1  (Citation Analysis)
연도 인용수 순위
1 K. Sugiyama, S Tagawa, M Toda, "Methods for Visual Understanding of Hierarchical System Stuctures," IEEE Transaction on Systems, Man and Cybernetics 11(2):109-125, 1981.   DOI   ScienceOn
2 Bing Zhang, Stefan Kirov and Jay Snody, "Web-Gestalt: and integrated system for exploring gene sets in various biological contexts," Nucleic Acis Research, Vol. 33, pp. 741-748, 2005   DOI   ScienceOn
3 Glynn Dennis Jr et al., "DAVID: Database for Annotation, Visualization, and Interated Disco-Annotation, Visualization, and Integrated Discovery," Genome Biology, Vol.4, Num.5, pp.3, 2003.   DOI
4 Vidar Beisvag et al., "GeneTools - application for functional annotation and statistical hypothesis testing," BMC Bioinformatice, Vol.7, pp.470, 2006.   DOI   PUBMED
5 Homin K Lee, William Braynen, Kiran Keshav and Paul Pavlidis, "ErmineJ: Tool for functional analysis of gene expression data sets," BMC Bioinformatis, Vol.6, pp. 269, 2005.   DOI   PUBMED
6 Rachel SG Sealfon, Matthew A Hibbs, Curtis Huttenhower, Chad L Myers and Olga G Troyanskaya, "GOLEM: an interactive graph-based gene-ontology navigation and analysis tool," BMC Bioinformatice, Vol.7, pp. 443, 2006.   DOI   PUBMED
7 P. Eades, "A heruistic for graph drawing," Congressus Numerantium, Vol. 42, pp. 149-160, 1984.
8 Dong-Soo Han, Suk-Hoon Jung, Woo-Hyuk Jang, and Choon-Ho Lee, "Constraints Based Dynamic Protein Interaction Network," 한국정보과학회, 2005.
9 Yannis Tzitzikas, JeanLuc Hainaut, "On the Visualization of Large sized Ontologies," AVI, pp. 99-102, 2006.
10 Steven Maere, Karel Heymans and Martin Kuiper, "BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks," Bioinformatics, 2005   DOI   PUBMED   ScienceOn
11 SunLee Bang, JaeHun Choi, JongMin Park, SooJun Park, "단백질 상호작용 네트워크의 개념 분류 레이아웃", 한국정보과학회 학술발표논문집, pp. 61-63 (3 pages), 2006.   과학기술학회마을
12 Aaron Kershenbaum, Keiha Murray, "Visualization of network structures," Journal of Computing Sciences in Colleges, Volume 21, Issue 2, Pages: 59-71, 2005.
13 Mi-Kyung Lee and Ki-Bong Kim, "A Visualization and Inference System for Protein-Protein Interaction," 한국정보과학회, 2004.
14 http://www.meta-biz.net/html/product03.htm
15 Bobby-Joe Breitkreutz, Chris Stark, Mike Tyers. "Osprey: a network visualization system," Genome Biology, 2003.   PUBMED
16 Hee-Jeong Jin, Ji-Hyun Yoon, and Hwan-Gue Cho, "An Analysis System for Protein-Protein Interaction Data Based on Graph Theory," 한국정보과학회, 2006.
17 Ivan Herman, Guy Melancon, M. Scott Marshall, "Graph Visualization and Navigation in Information Visualization: A Survey." IEEE Transactions on Visualization and Computer Graphics, Vol.6, No.1, pp. 24-43, January 2000.   DOI   ScienceOn
18 Benno Schwikowski, Peter Uetz, Stanley Fields, "A network of protein-protein interactions in yeast," Nature Biotechnology 18, 1257-1261, 2000.   DOI   PUBMED   ScienceOn