Biochem. J. (2004) 381
(1–12) (Printed in Great Britain)
Review article
Charting gene regulatory networks: strategies, challenges and perspectives
Gong-Hong WEI, De-Pei LIU1 and Chih-Chuan LIANG
National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences (CAMS) and Peking Union Medical College (PUMC), 5 Dong Dan San Tiao, Beijing 100005, P.R. China
One of the foremost challenges in the post-genomic era will be to chart the gene regulatory networks of cells, including aspects such as genome annotation, identification of cis-regulatory elements and transcription factors, information on protein–DNA and protein–protein interactions, and data mining and integration. Some of these broad sets of data have already been assembled for building networks of gene regulation. Even though these datasets are still far from comprehensive, and the approach faces many important and difficult challenges, some strategies have begun to make connections between disparate regulatory events and to foster new hypotheses. In this article we review several different genomics and proteomics technologies, and present bioinformatics methods for exploring these data in order to make novel discoveries.
Key words: bioinformatics, cis-regulatory code, data processing, functional genomics and proteomics, gene regulatory network, protein–DNA and protein–protein interaction.
Abbreviations used: ChIP-chip, chromatin immunoprecipitation–DNA microarray; FFL, feed-forward loop; GRN, gene regulatory network; MALDI-TOF, matrix-assisted laser desorption/ionization time-of-flight; ORF, open reading frame; NF-kB, nuclear factor-kB; SBML, System Biology Markup Language; SBW, System Biology Workbench; TAP, tandem affinity purification; TF, transcription factor; XML, eXtensible Makeup Language; Y2H, yeast two-hybrid.
1To whom correspondence should be addressed (e-mail liudp@pumc.edu.cn).
Received 27 February 2004/13 April 2004; accepted 13 April 2004
Published as BJ Immediate Publication 13 April 2004, DOI 10.1042/BJ20040311
The Biochemical Society, London ©2004
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