Nucleotide variation of regulatory motifs may lead to distinct expression patterns

Bioinformatics

Volumn 23, Issue 13, 2007, Pages

  Segal, Liat ^a   Lapidot, Michal ^b   Solan, Zach ^a   Ruppin, Eytan ^a   Pilpel, Yitzhak ^b   Horn, David ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; NUCLEOTIDE; TRANSCRIPTION FACTOR;

ANALYTIC METHOD; CALCULATION; CLUSTER ANALYSIS; CONFERENCE PAPER; CONSENSUS SEQUENCE; CONTROLLED STUDY; GENE CLUSTER; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE FUNCTION; GENETIC CORRELATION; GENETIC SIMILARITY; GENETIC VARIABILITY; MOLECULAR BIOLOGY; NONHUMAN; NUCLEOTIDE BINDING SITE; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN MOTIF; SACCHAROMYCES CEREVISIAE; SINGLE NUCLEOTIDE POLYMORPHISM;

SACCHAROMYCES CEREVISIAE;

EID: 34547844125     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm183     Document Type: Conference Paper

References (31)

1. Ashburner, M. et al. (2000) Gene ontology: Tool for the unification of biology, 25, 25-29.
2. Bailey, TL. and Elkan, C. (1995) The value of prior knowledge in discovering motifs with MEME. Proc. Int. Conf. Intell. Syst. Mol. Biol., 3, 21-29.
3. Barash, Y. et al. (2003) Modeling Dependencies in Protein-DNA Binding Sites. RECOMB, Berlin, Germany, pp. 28-37.
4. Benjamini, Y. and Hochberg, Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc., Series B (Methodological), 57, 289-300.
5. Benos, P.V. et al. (2002) Additivity in protein-DNA interactions: holy good an approximation is it? Nucleic Acids Res., 30, 4442-4451.
6. Berg, O.G. and von Hippel, P.H. (1987) Selection of DNA binding sites by regulatory proteins: Statistical-mechanical theory and application to operators and promoters. J. Mol. Biol., 193, 729-743.
7. Boyle, E.I. et al. (2004) GO::TermFinder - open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes. Bioinformatics, 20, 3710-3715.
8. Brazma, A. et al. (1998) Predicting gene regulatory elements in silico on a genomic scale. Genome Res., 8, 1202-1215.
9. Bulyk, M.L. et al. (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res., 30, 1255-1261.
10. Bussemaker, H.J. et al. (2000) Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc. Natl Acad. Sci. USA, 97, 10096-10100.
11. Dermitzakis, E.T. and Clark, A.G. (2002) Evolution of transcription factor binding sites in mammalian gene regulatory-regions: Conservation and turnover. Mol. Biol. Evol., 19, 1114-1121.
12. Durbin, R. et al. (1998) Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, Cambridge.
13. Gasch, A.P. et al. (2000) Genomic expression programs in the response of yeast cells to environmental changes. Mol. Biol. Cell, 11, 4241-4257.
14. Harbison, C.T. et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature, 431, 99-104.
15. Koch, C. et al. (1993) A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science, 261, 1551-1557.
16. Lawrence, C. et al. (1993) Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment. Science, 262 208-214.
17. Lapidot, M. and Pilpel, Y. (2003) Comprehensive quantitative analyses of the effects of promoter sequence elements on mRNA transcription. Nucleic Acids Res., 31, 3824-3828.
18. Lefstin, J.A. and Yamamoto, K.R. (1998) Allosteric effects of DNA on transcriptional regulators. Nature, 392, 885-888.
19. Leung, T.H. et al. (2004) One nucleotide in a [kappa]B site can determine cofactor specificity for NF-[kappa]B directs. Cell, 118, 453-464.
20. Pavesi, G. et al. (2004) Weeder Web: Discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Res., 32, W199-W203.
21. Pilpel, Y. et al. (2001) Identifying regulatory networks by combinatorial analysis of promoter elements. Nat. Genet., 29 153-159.
22. Pritsker, M. et al. (2004) Whole-genome discovery of transcription factor binding sites by network-level conservation 10.1101/gr.1739204. Genome Res., 14, 99-108.
23. Roth, F.P, et al. (1998) Finding DNA regulatory motifs within unaligned non-coding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol., 16, 939-945.
24. Segal, E. et al. (2006) A genomic code for nucleosome positioning. Nature, 442, 772-778.
25. Shalgi, R. et al. (2005) A catalog of stability-associated sequence elements in 3′ UTRs of yeast mRNAs. Genome Biol., 6 R86.
26. Sinha, S. and Tompa, M. (2003) YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res., 31, 3586-3588.
27. Solan, Z, et al. (2005) Unsupervised learning of natural languages. Proc. Natl Acad. Sci. USA, 102, 11629-11634.
28. Stormo, G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
29. Sudarsanam, P. et al. (2002) Genome-wide co-occurrence of promoter elements reveals a cis-regulatory cassette of rRNA transcription motifs in Sacecharomyces cerevisiae. Genome Res., 12, 1723-1731.
30. Tavazoie, S. et al. (1999) Systematic determination of genetic network architecture. Nat. Genet., 22, 281-285.
31. Tomovic, A. and Oakeley, E.J, (2007) Position dependencies in transcription factor binding sites. Bioinformatics, 23, 933-41.