Nucleic Acids Research, 2007, Vol. 35, Web Server issue W251 algorithm, we recommend that the scores are best used as rankings rather than signiﬁcance measures. For this reason, a multiple testing correction is not applied as it does not alter the relative ranks. Empirically, we determined that TFBS proﬁles with Z-scores >10 and Fisher scores <0.01 facilitate the identiﬁcation of relevant TFBSs for our sets of reference genes (1). However, these are relatively stringent thresholds, and we encourage users to examine the scores of top-ranked TFBS proﬁles before applying any cutoﬀs. We provide a consistent display for all four systems. However, there are slight diﬀerences between the systems, such as diﬀerent parameters for selection on the input pages which are relevant for each species database and system. Also, due to the longer processing times required to compute combinations of TFBSs, Human CSA queues the analysis request on the server and emails the completed results to the user. CONCLUSIONS The oPOSSUM system is under continued development. Eﬀorts are underway to allow users to submit custom TF proﬁles to be included in the analysis. An improved search method for nuclear hormone receptors, which typically contain two half sites separated by a variable length spacer, has been developed and will be included in a future release. We will continue to add TFBS proﬁles as they become available, with an emphasis on expanding the repertoire of worm TFBS proﬁles. We believe the oPOSSUM web server is and will continue to be a useful resource for inference of mechanisms of co-regulation based on observed co-expression. SUPPLEMENTARY DATA Supplementary Data are available at NAR Online. ACKNOWLEDGEMENTS Project funding provided through the Canadian Institutes of Health Research (CIHR) and Merck. A.T.K. and S.J.H.S. are supported by the National Science and Engineering Research Council of Canada (NSERC); D.L.F., S.J.H.S. and W.W.W. are supported by the Michael Smith Foundation for Health Research (MSFHR); and D.L.F. and W.W.W. are supported by the CIHR. The authors would like to thank Jonathan Lim and Miroslav Hatas for systems support. The Open Access publication charge for this paper has been waived by Oxford University Press – NAR Editorial Board members are entitled to one free paper per year in recognition of their work on behalf of the journal. Conﬂict of interest statement. None declared. REFERENCES 1. Ho Sui,S.J., Mortimer,J.R., Arenillas,D.J., Brumm,J., Walsh,C.J., Kennedy,B.P. and Wasserman,W.W. (2005) oPOSSUM: identiﬁcation of over-represented transcription factor binding sites in co-expressed genes. Nucleic Acids Res., 33, 3154–3164. 2. Huang,S.S., Fulton,D.L., Arenillas,D.J., Perco,P., Ho Sui,S.J., Mortimer,J.R. and Wasserman,W.W. 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