@article{d2cdfb4c64b241d18a93eff66d1d77ea,
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.",
author = "Daniel Hurley and Hiromitsu Araki and Yoshinori Tamada and Ben Dunmore and Deborah Sanders and Sally Humphreys and Muna Affara and Seiya Imoto and Kaori Yasuda and Yuki Tomiyasu and Kosuke Tashiro and Christopher Savoie and Vicky Cho and Stephen Smith and Satoru Kuhara and Satoru Miyano and Charnock-Jones, {D. Stephen} and Crampin, {Edmund J.} and Print, {Cristin G.}",
note = "Funding Information: Research collaboration agreements between the University of Cambridge and GNI Ltd for generation of the endothelial cell data used in this work, and the implementation of Bayesian gene network inference methods; the University of Auckland Doctoral Scholarship (to D.H.); Maurice Wilkins Centre for Molecular Biodiscovery Studentship (to D.H.); Auckland Bioengineering Institute (to D.H.); Marsden Fund of the Royal Society of New Zealand (06-UOA-182 to E.J.C.); University of Auckland Early Career Research Excellence Award (#3606318 to E.J.C.); Health Research Council of New Zealand International Investment Opportunities Fund (06/581 to C.P.); University of Auckland Faculty of Medical and Health Sciences Research Development Fund (# 8303460 to C.P.); University of Auckland Vice-Chancellor{\textquoteright}s Development Fund (# 23285 to C.P.); Maurice Wilkins Centre of Research Excellence Fund. Funding for open access charge: Departmental Grant funding. Funding Information: We wish to thank the patients and staff at Rosie Hospital, Cambridge, UK, for their donation and collection of umbilical cords used to isolate HUVECs. Computation for the SiGN-BN method was provided by the Super Computer System, Human Genome Centre, Institute of Medical Science, University of Tokyo. We wish to thank Manjunath Kustagi and Andrea Califano of the Califano lab at Columbia University for their assistance with configuration and optimization for the ARACNE algorithm, and Alexander Hartemink and Eric Jarvis of Duke University for their assistance with configuration and optimization for the BANJO algorithm. Generation of the microarray data was supported by research collaboration agreements between the University of Cambridge and GNI Ltd. We also wish to thank Atsushi Doi and Masao Nagasaki for assistance with gene network digraph mapping using the Cell Illustrator application.",
year = "2012",
month = mar,
doi = "10.1093/nar/gkr902",
language = "English",
volume = "40",
pages = "2377--2398",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Oxford University Press",
number = "6",
}