MotEvo: Integrated bayesian probabilistic methods for inferring regulatory sites and motifs on multiple alignments of DNA sequences

Bioinformatics

Volumn 28, Issue 4, 2012, Pages 487-494

  Arnold, Phil ^a   Erb, Ionas ^b   Pachkov, Mikhail ^a   Molina, Nacho ^c   Van Nimwegen, Erik ^a  

^a UNIVERSITY OF BASEL   (Switzerland)

^b UNIVERSITAT POMPEU FABRA   (Spain)

^c EPFL   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ANIMAL; ARTICLE; BAYES THEOREM; BINDING SITE; ENHANCER REGION; HUMAN; METABOLISM; METHODOLOGY; NUCLEOTIDE SEQUENCE; PHYLOGENY; PROTEIN BINDING; SEQUENCE ALIGNMENT;

ANIMALS; BASE SEQUENCE; BAYES THEOREM; BINDING SITES; ENHANCER ELEMENTS, GENETIC; HUMANS; PHYLOGENY; PROTEIN BINDING; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS;

EID: 84857180279     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr695     Document Type: Article

References (37)

1. Arnosti, D.N. and Kulkarni, M.M. (2005) Transcriptional enhancers: intelligent enhanceosomes or flexible billboards? J. Cell Biochem., 94 890-898.
2. Bailey, T. and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Sec. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
3. Bulyk, M.L. (2003) Computational prediction of transcription-factor binding site locations. Genome Biol., 5, 201.
4. Carmack, C.S. et al. (2007) PhyloScan: identification of transcription factor binding sites using cross-species evidence. Algor. Mol. Biol., 2, 1.
5. Chen, K. et al. (2010) Correlating gene expression variation with cis-regulatory polymorphism in Saccharomyces cerevisiae. Genome Biol. Evol., 2, 697-707.
6. Davidson, E.H. (2001) Genomic Regulatory Systems. Academic Press, San Diego.
7. Durbin, R. et al. (1998) Biological Sequence Analysis. Cambridge, UK.
8. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17, 368-376.
9. Frith, M.C. et al. (2001) Detection of cis-element clusters in higher eukaryotic DNA. Bioinformatics, 17, 878-889.
10. Halpern, A.L. and Bruno, W.J. (1998) Evolutionary distances for protein-coding sequences: modeling site-specific residue frequencies. Mol. Biol. Evol., 5, 910-917.
11. Hannenhalli, S. (2008) Eukaryotic transcription factor binding sites-modeling and integrative search methods. Bioinformatics, 24, 1325-1331.
12. Hawkins, J. et al. (2009) Assessing phylogenetic motif models for predicting transcription factor binding sites. Bioinformatics, 25, i339-i347.
13. Holohan, E.E. et al. (2007) CTCF genomic binding sites in Drosophila and the organisation of the bithorax complex. PLoS Genet., 3, e112.
14. Ivan, A. et al. (2008) Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs. Genome Biol., 9, R22.
15. Jothi, R. et al. (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res., 36, 5221-5231.
16. Karolchik, D. et al. (2008) The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res., 36, D773-D779.
17. Kellis, M. et al. (2003) Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature, 423, 241-254.
18. Lawrence, C.E. et al. (1993) Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment. Science, 262, 208-214.
19. McBride, K.M. and Reich, N.C. (2003) The ins and outs of STAT1 nuclear transport. Sci. STKE, 2003, RE13.
20. Molina, N. and van Nimwegen, E. (2008) Universal patterns of purifying selection at noncoding positions in bacteria. Genome Res., 18, 148-160.
21. Moses, A.M. et al. (2004) MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol., 5, R98.
22. Notredame, C. et al. (2000) T-Coffee: a novel method for multiple sequence alignments. J. Mol. Biol., 302, 205-217.
23. Palumbo, M.J. and Newberg, L.A. (2010) Phyloscan: locating transcription-regulating binding sites in mixed aligned and unaligned sequence data. Nucleic Acids Res., 38, W268-W274.
24. Rajewsky, N. et al. (2002) Computational detection of genomic cis-regulatory modules, applied to body patterning in the early drosophila embryo. BMC Bioinformatics, 3; doi:10.1186/1471-2105-3-30.
25. Roider, H.G. et al. (2007) Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics, 23, 134-141.
26. Schneider, T.D. and Stephens, R.M. (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res., 18, 6097-6100.
27. Siddharthan, R. et al. (2005) Phylogibbs: a Gibbs sampling motif finder that incorporates phylogeny. PLoS Comput. Biol., 1, e67.
28. Siepel, A. et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15, 1034-1050.
29. Sinha, S. et al. (2003) A probabilistic method to detect regulatory modules. Bioinformatics, 19 (Suppl. 1), i292-i301.
30. Sinha, S. et al. (2004) PhyME: a probabilistic algorithm for finding motifs in sets of orthologous sequences. BMC Bioinformatics, 5, 170.
31. Suzuki, H. et al. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet., 41, 553-562.
32. Valouev, A. et al. (2008) Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat. Methods, 5, 829-834.
33. van Nimwegen, E. (2007) Finding regulatory elements and regulatory motifs: a general probabilistic framework. BMC Bioinformatics, 8 (Suppl. 6), S4.
34. Vlieghe, D. et al. (2006) A new generation of JASPAR, the open-access repository for transcription factor binding site profiles. Nucleic Acids Res., 34, D95-D97.
35. Wasson, T. and Hartemink, A.J. (2009) An ensemble model of competitive multi-factor binding of the genome. Genome Res., 19, 2101-2112.
36. Wilczynski, B. and Furlong, E.E. (2010) Dynamic CRM occupancy reflects a temporal map of developmental progression. Mol. Syst. Biol., 6, 383.
37. Zhang, Y. et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biol., 9, R137.