ChIP-chip: Algorithms for calling binding sites

Methods in Molecular Biology

Volumn 556, Issue , 2009, Pages 165-175

  Liu, X Shirley ^a   Meyer, Clifford A ^a  

^a HARVARD SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

ChIP chip; normalization; peak detection; probe modeling

Indexed keywords

ALGORITHM; ANIMAL; ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER PROGRAM; DNA MICROARRAY; GENOME; HUMAN; INFORMATION RETRIEVAL; INSTRUMENTATION; METHODOLOGY;

ALGORITHMS; ANIMALS; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; GENOME; HUMANS; INFORMATION STORAGE AND RETRIEVAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 70349576551     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-60327-192-9_12     Document Type: Article

References (13)

1. Ren, B., Robert, F., Wyrick, J.J., Aparicio, O., Jennings, E.G., Simon, I., Zeitlinger, J., Schreiber, J.,Nannett, N., Kanin, E., Volkert, T.L., Wilson, C.J., Bell, S.R., Young, R.A. (2000) Genome-wide location and function of DNA binding proteins. Science 290, 2306-2309
2. Iyer, V.R.,Horak, C.E., Scafe, C.S., Botstein, D., Snyder, M., Brown, P.O. (2001) Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 409, 533-538
3. Lieb, J.D., Liu, X., Botstein, D., Brown, P.O. (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet. 208, 327-334
4. Horak, C.E., Mahajan, M.C., Luscombe, N.M., Gerstein, M., Weissman, S.M., Snyder, M. (2002) GATA-1 binding sites mapped in the b-globin locus by using mammalian ChIP-chip analysis. Proc Natl Acad Sci. 99, 2924-2929
5. Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J., Williams, A.J., Wheeler, R., Wong, B., Drenkow, J., Yamanaka, M., Patel, S., Brubaker, S., Tammana, H., Helt, G., Struhl, K., Gingeras, T.R. (2004) Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116, 499-509
6. Johnson, W., Li, W., Meyer, C. Gottardo, R., Carroll, J., Brown, M., Liu, X. (2006) Model-based analysis of tiling-arrays for ChIP-chip. Proc Nat Acad Sci USA 103, 12457-12462
7. Carroll, J.S., Liu, X.S., Brodsky, A.S., Li, W., Meyer, C.A., Szary, A.J., Eeckhoute, J., Shao, W., Hestermann, E.V., Geistlinger, T.R., Fox, E.A., Silver, P.A., Brown, M. (2005) Chromosome-wide mapping of estrogen receptor binding reveals longrange regulation requiring the forkhead protein FoxA1. Cell 122, 33-43
8. Zheng, Y., Josefowicz, S.Z., Kas, A., Chu, T.T., Gavin, M.A., Rudensky, A.Y. (2007) Genome-wide analysis of Foxp3 target genes in developing and mature regulatory T cells. Nature 445, 936-940
9. Wendt, K.S., Yoshida, K., Itoh, T., Bando, M., Koch, B., Schirghuber, E., Tsutsumi, S., Nagae, G., Ishihara, K., Mishiro, T., Yahata, K., Imamoto, F., Aburatani, H., Nakao, M., Imamoto, N., Maeshima, K., Shirahige, K., Peters, J.M. (2008) Cohesin mediates transcriptional insulation by CCCTC-binding factor. Nature 451, 796-801
10. Song, J.S., Johnson, W.E., Zhu, X., Zhang, X., Li, W., Manrai, A.K., Liu, J.S., Chen, R., Liu, X.S. (2007) Model-based analysis of two-color arrays (MA2C). Genome Biol. 8 Article R178, http://genomebiology. com/2007/8/8/R178
11. Carroll, J.S., Meyer, C.A., Song, J., Li, W., Geistlinger, T.R., Eeckhoute, J., Brodsky, A.S., Keeton, E.K., Fertuck, K.C., Hall, G.F., Wang, Q., Bekiranov, S., Sementchenko, V., Fox, E.A., Silver, P.A., Gingeras, T.R., Liu, X.S., Brown, M. (2006) Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 38, 1289-1297
12. Benson, G. (1999) Tandem repeats finder: A program to analyze DNA sequences. Nucleic Acids Res. 27, 573-580.
13. Bailey, J.A., Yavor, A.M., Massa, H.F., Trask, B.J., Eichler, E.E. (2001) Segmental duplications: Organization and impact within the current human genome project assembly. Genome Res. 11, 1005-1017.