MotifMap: A human genome-wide map of candidate regulatory motif sites

Bioinformatics

Volumn 25, Issue 2, 2009, Pages 167-174

  Xie, Xiaohui ^a,b   Rigor, Paul ^a,b   Baldi, Pierre ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BAYES THEOREM; COMPUTER PROGRAM; CONTROLLED STUDY; GENE MAPPING; GENE REGULATORY NETWORK; GENETIC CONSERVATION; GENETIC DATABASE; GENETIC REGULATION; GENOME ANALYSIS; HUMAN; HUMAN GENOME; INFORMATION PROCESSING; INFORMATION RETRIEVAL; INTERMETHOD COMPARISON; NONHUMAN; PRIORITY JOURNAL; REGULATORY SEQUENCE; SINGLE NUCLEOTIDE POLYMORPHISM; WEB BROWSER;

MAMMALIA;

EID: 58349110961     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn605     Document Type: Article

References (28)

1. Barski,A. et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
2. Efimenko,E. et al. (2005) Analysis of xbx genes in C. elegans. Development, 132, 1923-1934.
3. Elemento,O. and Tavazoie,S. (2005) Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biol., 6, R18.
4. Ettwiller,L. et al. (2005) The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates. Genome Biol., 6, R104.
5. Frazer,K.A. et al. (2007)Asecond generation human haplotype map of over 3.1 million SNPs. Nature, 449, 851-861.
6. Johnson,D.S. et al. (2006) Genome-wide mapping of in vivo protein-DNA interactions. Science, 316, 1497-1502.
7. Karolchik,D. et al. (2003) The UCSC Genome Browser Database. Nucleic Acids Res., 31, 51-54.
8. King,D.C. (2007) Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data. Genome Res., 17, 775-786.
9. Kim,T.H. et al. (2007) Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell, 128, 1231-1245.
10. Li,X. and Wong,W.H. (2005) Sampling motifs on phylogenetic trees. Proc. Natl Acad. Sci. USA, 102, 9481-9486.
11. Lim,C.A. et al. (2005) Genome-wide mapping of RELA(p65) binding identifies E2F1 as a transcriptional activator recruited by NF-kappaB upon TLR4 activation. Mol. Cell, 27, 622-635.
12. Lusk,R.W. and Eisen,M.B. (2008) Use of an evolutionary model to provide evidence for a wide heterogeneity of required affinities between transcription factors and their binding sites in yeast. Pac. Symp. Biocomput., 13, 489-500.
13. Margulies,E.H. et al. (2005) An initial strategy for the systematic identification of functional elements in the human genome by low-redundancy comparative sequencing. Proc. Natl Acad. Sci. USA, 102, 4795-4800.
14. Miller,W. et al. (2007) 28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res., 17 1797-1808.
15. 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.
16. Robertson,G. et al. (2007) Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat. Methods, 8, 651-657.
17. Sabeti,P.C. et al. (2007) Genome-wide detection and characterization of positive selection in human populations. Nature 449, 913-918.
18. Sandelin,A. et al. (2004) JASPAR: An open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res. 32, D91-D94.
19. Siddharthan,R. and van Nimwegen,E. (2007) Detecting regulatory sites using PhyloGibbs. Methods Mol. Biol., 395, 381-402.
20. Siepel,A. and Haussler,D. (2004) Combining Phylogenetic and Hidden Markov Models in Biosequence Analysis. J. Comput. Biol., 11, 413-428.
21. Siepel,A. et al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res., 15 1034-1050.
22. Stark,A. et al. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature, 450 219-232.
23. Wang,E.T. et al. (2006) Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc. Natl Acad. Sci. USA, 103, 135-140.
24. Wei,C.L. et al. (2006) A global map of p53 transcription-factor binding sites in the human genome. Cell, 124, 207-219.
25. Wingender,E. et al. (1996) TRANSFAC: A database on transcription factors and their DNA binding sites. Nucleic Acids Res., 24, 238-241.
26. Xie,X. et al. (2005) Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature 434, 338-345.
27. Xie,X. et al. (2007) Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc. Natl Acad. Sci. USA, 104, 7145-7150.
28. Zeller,K.I. et al. (2006) Global mapping of c-Myc binding sites and target gene networks in human B cells. Proc. Natl Acad. Sci. USA 47, 17834-17839.