title: Gene network inference and visualization tools for biologists: application to new human transcriptome datasets.
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.
authors: 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.
authors: Daniel
authors: D
authors: Hurley
authors: Hiromitsu
authors: H
authors: Araki
authors: Yoshinori
authors: Y
authors: Tamada
authors: Ben
authors: B
authors: Dunmore
authors: Deborah
authors: D
authors: Sanders
authors: Sally
authors: S
authors: Humphreys
authors: Muna
authors: M
authors: Affara
authors: Seiya
authors: S
authors: Imoto
authors: Kaori
authors: K
authors: Yasuda
authors: Yuki
authors: Y
authors: Tomiyasu
authors: Kosuke
authors: K
authors: Tashiro
authors: Christopher
authors: C
authors: Savoie
authors: Vicky
authors: V
authors: Cho
authors: Stephen
authors: S
authors: Smith
authors: Satoru
authors: S
authors: Kuhara
authors: Satoru
authors: S
authors: Miyano
authors: D Stephen
authors: DS
authors: Charnock-Jones
authors: Edmund J
authors: EJ
authors: Crampin
authors: Cristin G
authors: CG
authors: Print
mesh_terms: D002478:Cells, Cultured; D003196:Computer Graphics; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D061307:Human Umbilical Vein Endothelial Cells / Q000187:drug effects / Q000378:metabolism; D006801:Humans; D016328:NF-kappa B / Q000378:metabolism; D052002:NF-kappa B p50 Subunit / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis; D034741:RNA, Small Interfering; D012984:Software; D014409:Tumor Necrosis Factor-alpha / Q000494:pharmacology
chemical_list: D016328:NF-kappa B; D052002:NF-kappa B p50 Subunit; D034741:RNA, Small Interfering; D014409:Tumor Necrosis Factor-alpha