Mining ChIP-chip data for transcription factor and cofactor binding sites

Bioinformatics

Volumn 21, Issue SUPPL. 1, 2005, Pages

  Smith, Andrew D ^a   Sumazin, Pavel ^a,b   Das, Debopriya ^a   Zhang, Michael Q ^a  

^a Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

^b Portland State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CYTIDINE DIPHOSPHATE; NUCLEAR FACTOR I; TRANSCRIPTION FACTOR;

ARTICLE; BINDING SITE; CONTROLLED STUDY; GENE EXPRESSION; GENETIC ALGORITHM; LIVER; METHODOLOGY; MULTIVARIATE ANALYSIS; PANCREAS ISLET; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PROTEIN MICROARRAY; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; REGRESSION ANALYSIS; TISSUE MICROARRAY; TISSUE SPECIFICITY;

CHIP-CHIP; COFACTOR BINDING; INTERACTION MODEL; MICROARRAY DATA; MOTIF DISCOVERY; MULTIVARIATE REGRESSION; PANCREATIC ISLET; RELATIVE POSITIONS;

FORECASTING; INTELLIGENT SYSTEMS; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE; REGRESSION ANALYSIS; TISSUE; TRANSCRIPTION FACTORS;

BINDING SITES;

EID: 84860506529     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1043     Document Type: Article

References (40)

1. Andres,V., Chiara,M.D. and Mahdavi,V. (1994) A new bipartite DNA-binding domain: Cooperative interaction between the cut repeat and homeo domain of the cut homeo proteins. Genes Dev., 8, 245-257.
2. Antes,T.J., Chen,J., Cooper,A.D. and Levy-Wilson,B. (2000) The nuclear matrix protein cdp represses hepatic transcription of the human cholesterol-7alpha hydroxylase gene. J. Biol. Chem., 275, 26649-26660.
3. Buhler,J. and Tompa,M. (2002) Finding motifs using random projections. J. Comput. Biol., 9, 225-242.
4. Bussemaker,H.J., Li,H. and Siggia,E.D. (2001) Regulatory element detection using correlation with expression. Nat. Genet., 27, 167-171.
5. Carey,M. (1998) The enhanceosome and transcriptional synergy. Cell, 92, 5-8.
6. Conlon,E.M., Liu,X.S., Lieb,J.D. and Liu,J.S. (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl Acad. Sci. USA, 100, 3339-3344.
7. Das,D., Banerjee,N. and Zhang,M. (2004) Interacting models of cooperative gene regulation. Proc. Natl Acad. Sci. USA, 101, 16234-16239.
8. Das,D. and Zhang,M.Q. Adaptively inferring cis-Regulatory Architecture in Human Genome, 2005. Submitted.
9. Du,K., Leu,J.I., Peng,Y. and Taub,R. (1998) Transcriptional upregulation of the delayed early gene HRS/SRp40 during liver regeneration. interactions among YY1, GA-binding proteins, and mitogenic signals. J. Biol. Chem., 273, 35208-35215.
10. Eskin,E. (2004) From profiles to patterns and back again: A branch and bound algorithm for finding near optimal motif profiles. In Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, San Diego, CA, March 27-31, 2004, 115-124. ACM Press.
11. Fickett,J.W. (1996) Coordinate positioning of mef2 and myogenin binding sites. Gene, 172, GC19-GC32.
12. Figueiredo,M.S. and Brownlee,G.G. (1995) Cis-acting elements and transcription factors involved in the promoter activity of the human factor VIII gene. J. Biol. Chem., 270, 11828-11838.
13. Friedman,J.H. (1991) Multivariate adaptive regression splines. Annals of Statistics, 19, 1-142.
14. Greil,F., van der Kraan,I., Delrow,J., Smothers,J.F., de Wit,E., Bussemaker,H.J., van Driel,R., Henikoff,S. and van Steensel,B. (2003) Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location. Genes Dev., 17, 2825-2838.
15. GuhaThakurta,D. and Stormo,G.D. (2001) Identifying target sites for cooperatively binding factors. Bioinformatics, 17, 608-621.
16. Hanlon,M., Bundy,L.M. and Sealy,L. (2000) C/EBP beta and Elk-1 synergistically transactivate the c-fos serum response element. BMC Cell Biol., 1, 20.
17. Hannenhalli,S. and Levy,S. (2002) Predicting transcription factor synergism. Nucleic Acids Res., 30, 4278-4284.
18. Hastie,T., Tibshirani,R. and Friedman,J.H. (2001) The Elements of Statistical Learning. Springer Verlag, NY.
19. Ishii,Y., Hansen,A.J. and Mackenzie,P.I. (2000) Octamer transcription factor-1 enhances hepatic nuclear factor-1alpha-mediated activation of the human UDP glucuronosyltransferase 2B7 promoter. Mol. Pharmacol., 57, 940-947.
20. Karlin,S. and Brendel,V. (1992) Chance and statistical significance in protein and DNA sequence analysis. Science, 257, 39-49.
21. Krivan,W. and Wasserman,W.W. (2001) A predictive model for regulatory sequences directing liver-specific transcription. Genome Res., 11, 1559-1966.
22. Ktistaki,E. and Talianidis,I. (1997) Modulation of hepatic gene expression by hepatocyte nuclear factor 1. Science, 277, 109-112.
23. Kullback,S. and Leibler,R.A. (1951) On information and sufficiency. Ann. Math. Stat., 22, 76-86.
24. Liu,J.S., Lawrence,C.E. and Neuwald,A. (1995) Bayesian models for multiple local sequence alignment and its Gibbs sampling strategies. J. Am. Stat. Assoc., 90, 1156-1170.
25. Liu,J.S., Liu,X. and Brutlag,D.L. (2001) Bioprospector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. In Proceedings of the Pacific Symposium on Biocomputing, Mauna Lani, Hawaii, Vol. 6, pp. 127-138.
26. Matys,V., Fricke,E., Geffers,R., Gossling,E., Haubrock,M., Hehl,R., Hornischer,K., Karas,D., Kel,A.E., Kel-Margoulis,O.V. et al. (2003) TRANSFAC(R): Transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
27. Odom,D.T., Zizlsperger,N., Gordon,D.B., Bell,G.W., Rinaldi,N.J., Murray,H.L., Volkert,T.L., Schreiber,J., Rolfe,P.A., Gifford,D.K. et al. (2004) Control of pancreas and liver gene expression by Hnf transcription factors. Science, 303, 1378-1381.
28. Pevzner,P. and Sze,S. (2000) Combinatorial approaches to finding subtle signals in DNA sequences. In Phil Bourne and Michael Gribskov, Chairs (ed.), Proceedings of the Annual International Symposium on Intelligent Systems for Molecular Biology, AAAI Press, La Jolla, CA, August 19-23, pp. 269-278.
29. Raymondjean,M., Pichard,A.L., Gregori,C., Ginot,F. and Kahn,A. (1991) Interplay of an original combination of factors: C/EBP, NFY, HNF3, and HNF1 in the rat aldolase B gene promoter. Nucleic Acids Res., 19, 6145-6153.
30. Ren,B. and Dynlacht,B.D. (2004) Use of chromatin immunoprecipitation assays in genome-wide location analysis of mammalian transcription factors. Meth. Enzymol, 376, 304-315.
31. Smith,A.D., Sumazin,P. and Zhang,M.Q. (2005) Identifying tissue-selective transcription factor binding sites in vertebrate promoters. Proc. Natl Acad. Sci. USA, 102, 1560-1565.
32. Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
33. Su,A.I., Wiltshire,T., Batalov,S., Lapp,H., Ching,K.A., Block,D., Zhang,J., Soden,R., Hayakawa,M., Kreiman,G. et al. (2004) A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl Acad. Sci. USA, 101, 6062-6067.
34. Thompson,W., Rouchka,E.C. and Lawrence,C.E. (2003) Gibbs recursive sampler: Finding transcription factor binding sites. Nucleic Acids Res., 31, 3580-3585.
35. Tronche,F., Ringeisen,F., Blumenfeld,M., Yaniv,M. and Pontoglio,M. (1997) Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J. Mol. Biol., 266, 231-245.
36. Uchida,C., Oda,T., Sugiyama,T., Otani,S., Kitagawa,M. and Ichiyama,A. (2002) The role of Sp1 and AP-2 in basal and protein kinase A-induced expression of mitochondrial serine: Pyruvate aminotransferase in hepatocytes. J. Biol. Chem., 277, 39082-39092.
37. Wasserman,W.W. and Fickett,J.W. (1998) Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol., 278, 167-181.
38. Wu,K., Wilson,D., Shih,C. and Darlington,G. (1994) The transcription factor HNF1 acts with C/EBP alpha to synergistically activate the human albumin promoter through a novel domain. J. Biol. Chem., 269, 1177-1182.
39. Xu,Y., Porntadavity,S. and St Clair,D.K. (2002) Transcriptional regulation of the human manganese superoxide dismutase gene: The role of specificity protein 1 (Sp1) and activating protein-2 (AP-2). Biochem. J., 362, 401-412.
40. Zhou,D.X. and Yen,T.S. (1991) The ubiquitous transcription factor Oct-1 and the liver-specific factor HNF-1 are both required to activate transcription of a hepatitis b virus promoter. Mol. Cell Biol., 11, 1353-1359.