Positional distribution of human transcription factor binding sites

Nucleic Acids Research

Volumn 36, Issue 21, 2008, Pages 6795-6805

  Koudritsky, Mark ^a   Domany, Eytan ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; DNA; HEPATOCYTE NUCLEAR FACTOR 1ALPHA; HEPATOCYTE NUCLEAR FACTOR 3BETA; HEPATOCYTE NUCLEAR FACTOR 4ALPHA; HEPATOCYTE NUCLEAR FACTOR 6; OCTAMER TRANSCRIPTION FACTOR 4; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR NANOG; TRANSCRIPTION FACTOR SOX2; UPSTREAM STIMULATORY FACTOR 1;

ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; GENE TARGETING; GENOME ANALYSIS; HUMAN; HUMAN CELL; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN LOCALIZATION; TRANSCRIPTION INITIATION SITE;

BASE COMPOSITION; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OLIGONUCLEOTIDE PROBES; PROMOTER REGIONS, GENETIC; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION, GENETIC;

EID: 57149102296     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn752     Document Type: Article

References (26)

1. Allison,D.B, Cui,X., Page,G.P. and Sabripour,M. (2006) Microarray data analysis: From disarray to consolidation and consensus. Nat. Rev. Genet., 7, 55-65.
2. Rodriguez,B.A. and Huang,T.H. (2005) Tilling the chromatin landscape: emerging methods for the discovery and profiling of protein-DNA interactions. Biochem. Cell. Biol., 83, 525-534.
3. Hertzberg,L., Zuk,O., Getz,G. and Domany,E. (2005) Finding motifs in promoter regions. J. Comput. Biol., 12, 314-330.
4. Kel,A.E., Gossling,E., Reuter,I., Cheremushkin,E., Kel-Margoulis,O.V. and Wigender,E. (2003) MATCH: A tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res., 31, 3576-3579.
5. Sharan,R., Ben-Hur,A. and Loots,G.G. (2004) Ovcharenko ICREME: cis-regulatory module explorer for the human genome. Nucleic Acids Res., 32, W253-W256.
6. Quandt,K., Frech,K., Karas,H., Wingender,E. and Werner,T. (1995) MatInd and MatInspector: New fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res., 23, 4878-4884.
7. Lodish,H., Berk,A., Zipursky,S.L., Matsudaira,P., Baltimore,D., and Darnell,J., (2000) Molecular Cell Biology, 4th edn. W. H. Freeman. New York.
8. Pfeifer,D., Kist,R., Dewar,K., Devon,K., Lander,E.S., Birren,B., Korniszewski,L., Back,E. and Scherer,G. (1999) Campomelic dysplasia translocation breakpoints are scattered over 1Mb proximal to SOX9: evidence for an extended control region. Am. J. Hum. Genet., 65 111-124.
9. Kimura-Yoshida,C., Kitajima,K., Oda-Ishii,I., Tian,E., Suzuki,M., Yamamoto,M., Suzuki,T., Kobayashi,M., Aizawa,S. and Matsuo,I. (2004) Characterization of the pufferfish Otx2 cis-regulators reveals evolutionarily conserved genetic mechanisms for vertebrate head specification. Development, 131, 57-71.
10. Tabach,Y., Brosh,R., Buganim,Y., Reiner,A., Zuk,O., Yitzhaky,A., Koudritsky,M., Rotter,V. and Domany,E. (2007) Wide-scale analysis of human functional transcription factor binding reveals a strong bias towards the transcription start site. PLoS ONE, 2, e807.
11. Xie,X.H., Lu,J., Kulbokas,E.J., Golub,T.R., Mootha,V., Lindblad-Toh, K., Lander,E.S. and Kellis,M. (2005) Systematic discovery of regulatory motifs in human promoters and 3[prime] UTRs by comparison of several mammals. Nature, 434, 338-345.
12. Cora,D., Herrmann,C., Dieterich,C., Di Cunto,F., Provero,P. and Caselle,M. (2005) Ab initio identi?cation of putative human transcription factor binding sites by comparative genomics. BMC Bioinformatics, 6, 110.
13. Boyer,L.A., Lee,T.I., Cole,M.F., Johnstone,S.E., Levine,S.S., Zucker,J.R., Guenther,M.G., Kumar,R.M., Murray,H.L., Jenner,R.G. et al. (2005) Core transcriptional regulatory circuitry in human embryonic stem cells. Cell, 122, 947-956.
14. Odom,D.T., Dowell,R.D., Jacobsen,E.S., Nekludova,L, Rolfe,P.A., Danford,T.W., Gifford,D.K., Fraenkel,E., Bell,G.I. and Young,R.A. (2006) Core transcriptional regulatory circuitry in human hepatocytes. Mol. Syst. Biol., 2, E1.
15. Chickarmane,V., Troein,C., Nuber,U.A., Sauro,H.M. and Peterson,C. (2006) Transcriptional dynamics of the embryonic stem cell switch. PLoS Comput. Biol., 2, e123.
16. Sengupta,A., Djordjevic,M. and Shraiman,B. (2002) Specificity and robustness in transcription control networks. Proc. Natl Acad. Sci. USA, 99, 2072-2077.
17. Boyer et al. http://jura.wi.mit.edu/young_public/hESregulation/ Technology.html, accompanying website of Boyer et al (Ref 13).
18. Qi,Y., Rolfe,A., MacIsaac,K.D., Gerber,G.K., Pokholok,D., Zeitlinger,J., Danford,T., Dowell,R.D., Fraenkel,E., Jaakkola,T.S. et al. (2006) High-resolution computational models of genome binding events. Nat. Biotechnol., 24, 963-970.
19. Subramanian,A., Tamayo,P., Mootha,V.K., Mukherjee,S., Ebert,B.L., Gillette,M.A., Paulovich,A., Pomeroy,S.L., Golub,T.R., Lander,E.S. et al. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl Acad. Sci., 102, 15545-15550.
20. Benjamini,Y. and Hochberg,Y. (1995) Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. R. Stat. Soc. Ser. B (Methodological), 57, 289-300.
21. Ashburner,M., Ball,C.A., Blake,J.A., Botstein,D., Butler,H., Cherry,J.M., Davis,A.P., Dolinski,K., Dwight,S.S., Eppig,J.T. et al. (2000) Gene ontology: Tool for the unification of biology. The gene ontology consortium. Nat. Genet., 25, 25-29.
22. Kent,W.J., Sugnet,C.W., Furey,T.S., Roskin,K.M., Pringle,T.H., Zahler,A.M. and Haussler,D. (2002) The human genome browser at UCSC. Genome Res., 12, 996-1006.
23. Weirauch,M. and Raney,B. TFBS conserved track at UCSC genome browser http://genome.ucsc.edu/cgi-bin/hgTrackUi?g=tfbsConsSites.
24. 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: Transcriptional regulation, from patterns to profiles. Nucleic Acids Res., 31, 374-378.
25. Eisenberg,E. and Levanon,E.Y. (2003) Human housekeeping genes are compact. Trends Genet., 19, 362-365.
26. Chew,J.L., Loh,Y.H., Zhang,W.S., Chen,X., Tam,W.L., Yeap,L.S., Li,P., Ang,Y.S., Lim,B., Robson,P. et al. (2005) Reciprocal transcriptional regulation of Pou5f1 and Sox2 via the Oct4/Sox2 complex in embryonic stem cells. Mol. Cell. Biol., 25, 6031-6046.