W524–W528 Nucleic Acids Research, 2006, Vol. 34, Web Server issue doi:10.1093/nar/gkl041 TFBScluster web server for the identification of mammalian composite regulatory elements Ian J. Donaldson and Berthold Go¨ ttgens* Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge, CB2 2XY, UK Received January 10, 2006; Revised and Accepted January 24, 2006 ABSTRACT Identification of transcriptional regulatory elements represents a critical step in our ability to recons- truct transcriptional regulatory networks from gene expression profiling datasets. To facilitate computa- tional identification of candidate gene regulatory elements from whole genome sequences, we have developed the TFBScluster web server that integrates several tools for the genome-wide identification and subsequent characterization of transcription factor binding site clusters that are conserved in multiple mammalian species. Either the human or mouse genomes can be used as the reference sequence with direct links from the search results to the ENSEMBL and UCSC genome browsers. Moreover, TFBScluster provides seamless integration of trans- cription factor binding site searches with genome annotation and gene expression profiling data, to allow prioritising computational predictions for subsequent experimental validation. TFBScluster is publicly available at http://hscl.cimr.cam.ac.uk/ TFBScluster_genome_portal.html. INTRODUCTION One of the great challenges of the post genomic era is to integrate the various ‘omics’ approaches with the accumulated data from traditional hypothesis driven research to make a ‘systems level’ understanding of biological processes a feasible goal. Systems biology ‘parts lists’ (e.g. whole genome sequences and gene expression proﬁles) are increasingly gen- erated for higher eukaryotes, including human and vertebrate model systems. Based on recent studies in sea urchins, ﬂies and worms (1–6), analysis of transcriptional gene regulatory networks holds particular promise for applying systems biology to higher eukaryotes. One particularly attractive feature of transcriptional regulatory networks lies in the fact that computational analysis of transcriptional regulatory networks should be facilitated since major components of the ‘parts lists’ will be intimately connected through a regul- atory code present in the genomic sequence that determines where, when and at what level each gene will be expressed. Nevertheless, the higher genomic and biological complexities of vertebrates currently pose major challenges to directly transferring approaches developed in lower eukaryotes. Identiﬁcation and subsequent characterization of gene regu- latory elements will be a key step in assembling transcriptional regulatory networks from gene expression proﬁling data, with the ultimate goal of unravelling the regulatory codes that gov- ern gene expression in various cell types. The resulting models of transcriptional regulatory networks will have the ability to elucidate system properties, which may not be apparent when studying individual components. Moreover, models can pre- dict the outcome of perturbations, experimental or patholo- gical, and are therefore likely to play a key role in future drug discovery. The network nodes of transcriptional regulatory networks consist of gene regulatory elements; these are stretches of DNA sequence containing multiple transcription factor binding sites (TFBSs) that act combinatorially on the transcriptional regulation of a given gene. Therefore, genome- wide analysis of regulatory elements is ultimately required to construct transcriptional regulatory networks. However, even more so than in simpler genomes such as ﬂy, yeast or worm, the complexity of mammalian genomes makes computational identiﬁcation of functional regulatory elements a formidable task. The DNA sequence motifs recognized by transcription factors are mostly short and degenerate, and regulatory elements can be located many kilobases away from the proximal promoter of a gene in distal 50 and 30 enhancers or in introns (7). To facilitate the identiﬁcation of mammalian gene regula- tory elements, we developed the TFBScluster tool for the genome-wide discovery of candidate regulatory elements and the genes under their control. The original version of TFBScluster was designed speciﬁcally for the characterization of gene regulatory elements active in human blood stem cells (8). In a proof of principle study, TFBScluster allowed *To whom correspondence should be addressed. Tel: +44 1223 336829; Fax: +44 1223 762670; Email: bg200@cam.ac.uk The Author 2006. Published by Oxford University Press. All rights reserved. The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org