Document Detail


Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era.
MedLine Citation:
PMID:  23281970     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
BACKGROUND: The overwhelming amount of network data in functional genomics is making its visualization cluttered with jumbling nodes and edges. Such cluttered network visualization, which is known as "hair-balls", is significantly hindering data interpretation and analysis of researchers. Effective navigation approaches that can always abstract network data properly and present them insightfully are hence required, to help researchers interpret the data and acquire knowledge efficiently. Cytoscape is a de facto standard platform for network visualization and analysis, which has many users around the world. Apart from its core sophisticated features, it easily allows for extension of the functionalities by loading extra plug-ins.
RESULTS: We developed NaviClusterCS, which enables researchers to interactively navigate large biological networks of ~100,000 nodes in a "Google Maps-like" manner in the Cytoscape environment. NaviClusterCS rapidly and automatically identifies biologically meaningful clusters in large networks, e.g., proteins sharing similar biological functions in protein-protein interaction networks. Then, it displays not all nodes but only preferable numbers of those clusters at any magnification to avoid creating the cluttered network visualization, while its zooming and re-centering functions still enable researchers to interactively analyze the networks in detail. Its application to a real Arabidopsis co-expression network dataset illustrated a practical use of the tool for suggesting knowledge that is hidden in large biological networks and difficult to be obtained using other visualization methods.
CONCLUSIONS: NaviClusterCS provides interactive and multi-scale network navigation to a wide range of biologists in the big data era, via the de facto standard platform for network visualization. It can be freely downloaded at http://navicluster.cb.k.u-tokyo.ac.jp/cs/ and installed as a plug-in of Cytoscape.
Authors:
Thanet Praneenararat; Toshihisa Takagi; Wataru Iwasaki
Publication Detail:
Type:  Journal Article; Research Support, Non-U.S. Gov't     Date:  2012-12-13
Journal Detail:
Title:  BMC genomics     Volume:  13 Suppl 7     ISSN:  1471-2164     ISO Abbreviation:  BMC Genomics     Publication Date:  2012  
Date Detail:
Created Date:  2013-01-03     Completed Date:  2013-06-12     Revised Date:  2013-07-11    
Medline Journal Info:
Nlm Unique ID:  100965258     Medline TA:  BMC Genomics     Country:  England    
Other Details:
Languages:  eng     Pagination:  S24     Citation Subset:  IM    
Affiliation:
Department of Computational Biology, University of Tokyo, Kashiwa, Chiba, 277-8568, Japan. thanet@cb.k.u-tokyo.ac.jp
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MeSH Terms
Descriptor/Qualifier:
Arabidopsis / genetics,  metabolism
Cluster Analysis
Computational Biology
Databases, Factual
Gene Regulatory Networks
Genomics*
Internet
Software*
User-Computer Interface
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