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Nucleic Acids Res. 2012 Mar;40(6):2377-98. doi: 10.1093/nar/gkr902. Epub 2011 Nov 24.

Gene network inference and visualization tools for biologists: application to new human transcriptome datasets.

Author information

1
Auckland Bioengineering Institute, Department of Molecular Medicine and Pathology, School of Medical Sciences, Faculty of Medical and Health Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.

Abstract

Gene regulatory networks inferred from RNA abundance data have generated significant interest, but despite this, gene network approaches are used infrequently and often require input from bioinformaticians. We have assembled a suite of tools for analysing regulatory networks, and we illustrate their use with microarray datasets generated in human endothelial cells. We infer a range of regulatory networks, and based on this analysis discuss the strengths and limitations of network inference from RNA abundance data. We welcome contact from researchers interested in using our inference and visualization tools to answer biological questions.

PMID:
22121215
PMCID:
PMC3315333
DOI:
10.1093/nar/gkr902
[Indexed for MEDLINE]
Free PMC Article

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