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


Type
Article
Change log
Authors
Hurley, Daniel 
Araki, Hiromitsu 
Tamada, Yoshinori 
Dunmore, Ben 
Sanders, Deborah 
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.

Description
Keywords
Cells, Cultured, Computer Graphics, Gene Expression Profiling, Gene Regulatory Networks, Human Umbilical Vein Endothelial Cells, Humans, NF-kappa B, NF-kappa B p50 Subunit, Oligonucleotide Array Sequence Analysis, RNA, Small Interfering, Software, Tumor Necrosis Factor-alpha
Journal Title
Nucleic Acids Res
Conference Name
Journal ISSN
0305-1048
1362-4962
Volume Title
40
Publisher
Oxford University Press (OUP)