ArticleBMC genomics2012
Integration of interactive, multi-scale network navigation approach with Cytoscape for functional genomics in the big data era.
Article in BMC genomics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
13 citing papers in PubMed, 20 citations in OpenAlex.
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Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe 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.
resultsWe 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.
conclusionsNaviClusterCS 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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.