Locating potential enhancer elements by comparative genomics using the EEL software (original) (raw)
Hallikas, O. et al. Genome-wide prediction of mammalian enhancers based on analysis of transcription-factor binding affinity. Cell124, 47–59 (2006). ArticleCASPubMed Google Scholar
Cameron, R.A. et al. An evolutionary constraint: Strongly disfavored class of change in DNA sequence during divergence of cis-regulatory modules. Proc. Natl. Acad. Sci. USA102, 11769–11774 (2005). ArticleCASPubMedPubMed Central Google Scholar
Tompa, M. et al. Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol.23, 137–144 (2005). ArticleCASPubMed Google Scholar
Bejerano, G. et al. Ultraconserved elements in the human genome. Science304, 1321–1325 (2004). ArticleCASPubMed Google Scholar
Nazina, A.G. & Papatsenko, D.A. Statistical extraction of Drosophila cis-regulatory modules using exhaustive assessment of local word frequency. BMC Bioinformatics4, 65 (2003). ArticlePubMedPubMed Central Google Scholar
Grad, Y.H., Roth, F.P., Halfon, M.S. & Church, G.M. Prediction of similarly-acting cis-regulatory modules by subsequence profiling and comparative genomics in D. melanogaster and D. pseudoobscura. Bioinformatics20, 2738–2750 (2004). ArticleCASPubMed Google Scholar
Segal, E. & Sharan, R. A discriminative model for identifying spatial cis-regulatory modules. J. Comput. Biol.12, 822–834 (2005). ArticleCASPubMed Google Scholar
Durbin, R., Eddy, S.R., Krogh, A. & Mitchison, G. Biological Sequence Analysis: probabilistic Models of Proteins and Nucleic Acids (Cambridge Univ. Press, Cambridge, 1998).
Berman, B.P. et al. Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc. Natl. Acad. Sci. USA99, 757–762 (2002). ArticleCASPubMedPubMed Central Google Scholar
Alkema, W.B., Johansson, O., Lagergren, J. & Wasserman, W.W. MSCAN: identification of functional clusters of transcription factor binding sites. Nucleic Acids Res.32, 169–176 (2004). Article Google Scholar
Sharan, R., Ovcharenko, I., Ben-Hur, A. & Karp, R.M. CREME: a framework for identifying cis-regulatory modules in human-mouse conserved segments. Bioinformatics19, i283–i291 (2003). ArticlePubMed Google Scholar
Donaldson, I.J. et al. Genome-wide identification of cis-regulatory sequences controlling blood and endothelial development. Hum. Mol. Gene.14, 595–601 (2005). ArticleCAS Google Scholar
Philippakis, A.A., He, F.S. & Bulyk, M.L. Modulefinder: a tool for computational discovery of cis regulatory modules. in Proc. of the Pacific Symp. of Biocomputing 519–530 (2005).
Blanchette, M. et al. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res.16, 656–668 (2006). ArticleCASPubMedPubMed Central Google Scholar
Zhou, Q. & Wong, W.H. CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc. Natl. Acad. Sci. USA101, 12114–12119 (2004). ArticleCASPubMedPubMed Central Google Scholar
Rajewsky, N., Vergassola, M., Gaul, U. & Siggia, E.D. Computational detection of genomic cis-regulatory modules applied to body patterning in the early Drosophila embryo. BMC Bioinformatics3, 30 (2002). ArticlePubMedPubMed Central Google Scholar
Sinha, S., van Nimwegen, E. & Siggia, E.D. A probabilistic method to detect regulatory modules. Bioinformatics, 19, i292–i301 (2003). ArticlePubMed Google Scholar
Bailey, T.L. & Noble, W.S. Searching for statistically significant regulatory modules. Bioinformatics19, 16–25 (2003). Article Google Scholar
Frith, M.C., Li, M.C. & Weng, Z. Cluster-Buster: finding dense clusters of motifs in DNA sequences. Nucleic Acids Res.31, 3666–3668 (2003). ArticleCASPubMedPubMed Central Google Scholar
Xie, X. et al. Systematic discovery of regulatory motifs in human promoters and 3′ UTRs by comparison of several mammals. Nature434, 338–345 (2005). ArticleCASPubMedPubMed Central Google Scholar
Wasserman, W.W. & Sandelin, A. Applied bioinformatics for the identification of regulatory elements. Nat. Rev. Genet.5, 276–287 (2004). ArticleCASPubMed Google Scholar
Sinha, S. et al. Cross-species comparison significantly improves genome-wide prediction of cis-regulatory modules in Drosophila. BMC Bioinformatics5, 129 (2004). ArticlePubMedPubMed Central Google Scholar
Vlieghe, D. et al. A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res.34, D95–D97 (2006). ArticleCASPubMed Google Scholar
Hallikas, O. & Taipale, J. High-throughput assay for determining specificity and affinity of protein-DNA binding interactions. Nat. Protoc. 10.1038/nprot2006. 33 (2006).