Literature DB >> 19488878

ChIP-Chip: algorithms for calling binding sites.

X Shirley Liu1, Clifford A Meyer.   

Abstract

Genome-wide ChIP-chip assays of protein-DNA interactions yield large volumes of data requiring effective statistical analysis to obtain reliable results. Successful analysis methods need to be tailored to platform specific characteristics such as probe density, genome coverage, and the nature of the controls. We describe the use of the respective software packages MAT and MA2C for the analysis of ChIP-chip data from one-color Affymetrix and two-color NimbleGen or Agilent tiling microarrays.

Entities:  

Mesh：

Year:  2009        PMID： 19488878      PMCID： PMC3609550          DOI： 10.1007/978-1-60327-192-9_12

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  13 in total

1.  Genome-wide location and function of DNA binding proteins.

Authors:  B Ren; F Robert; J J Wyrick; O Aparicio; E G Jennings; I Simon; J Zeitlinger; J Schreiber; N Hannett; E Kanin; T L Volkert; C J Wilson; S P Bell; R A Young
Journal:  Science       Date:  2000-12-22       Impact factor: 47.728

2.  Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF.

Authors:  V R Iyer; C E Horak; C S Scafe; D Botstein; M Snyder; P O Brown
Journal:  Nature       Date:  2001-01-25       Impact factor: 49.962

3.  Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association.

Authors:  J D Lieb; X Liu; D Botstein; P O Brown
Journal:  Nat Genet       Date:  2001-08       Impact factor: 38.330

4.  Segmental duplications: organization and impact within the current human genome project assembly.

Authors:  J A Bailey; A M Yavor; H F Massa; B J Trask; E E Eichler
Journal:  Genome Res       Date:  2001-06       Impact factor: 9.043

5.  Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs.

Authors:  Simon Cawley; Stefan Bekiranov; Huck H Ng; Philipp Kapranov; Edward A Sekinger; Dione Kampa; Antonio Piccolboni; Victor Sementchenko; Jill Cheng; Alan J Williams; Raymond Wheeler; Brant Wong; Jorg Drenkow; Mark Yamanaka; Sandeep Patel; Shane Brubaker; Hari Tammana; Gregg Helt; Kevin Struhl; Thomas R Gingeras
Journal:  Cell       Date:  2004-02-20       Impact factor: 41.582

6.  Model-based analysis of tiling-arrays for ChIP-chip.

Authors:  W Evan Johnson; Wei Li; Clifford A Meyer; Raphael Gottardo; Jason S Carroll; Myles Brown; X Shirley Liu
Journal:  Proc Natl Acad Sci U S A       Date:  2006-08-08       Impact factor: 11.205

7.  Genome-wide analysis of estrogen receptor binding sites.

Authors:  Jason S Carroll; Clifford A Meyer; Jun Song; Wei Li; Timothy R Geistlinger; Jérôme Eeckhoute; Alexander S Brodsky; Erika Krasnickas Keeton; Kirsten C Fertuck; Giles F Hall; Qianben Wang; Stefan Bekiranov; Victor Sementchenko; Edward A Fox; Pamela A Silver; Thomas R Gingeras; X Shirley Liu; Myles Brown
Journal:  Nat Genet       Date:  2006-10-01       Impact factor: 38.330

8.  Chromosome-wide mapping of estrogen receptor binding reveals long-range regulation requiring the forkhead protein FoxA1.

Authors:  Jason S Carroll; X Shirley Liu; Alexander S Brodsky; Wei Li; Clifford A Meyer; Anna J Szary; Jerome Eeckhoute; Wenlin Shao; Eli V Hestermann; Timothy R Geistlinger; Edward A Fox; Pamela A Silver; Myles Brown
Journal:  Cell       Date:  2005-07-15       Impact factor: 41.582

9.  GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis.

Authors:  Christine E Horak; Milind C Mahajan; Nicholas M Luscombe; Mark Gerstein; Sherman M Weissman; Michael Snyder
Journal:  Proc Natl Acad Sci U S A       Date:  2002-02-26       Impact factor: 11.205

10.  Cohesin mediates transcriptional insulation by CCCTC-binding factor.

Authors:  Kerstin S Wendt; Keisuke Yoshida; Takehiko Itoh; Masashige Bando; Birgit Koch; Erika Schirghuber; Shuichi Tsutsumi; Genta Nagae; Ko Ishihara; Tsuyoshi Mishiro; Kazuhide Yahata; Fumio Imamoto; Hiroyuki Aburatani; Mitsuyoshi Nakao; Naoko Imamoto; Kazuhiro Maeshima; Katsuhiko Shirahige; Jan-Michael Peters
Journal:  Nature       Date:  2008-01-30       Impact factor: 49.962
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  2 in total

1.  STEME: efficient EM to find motifs in large data sets.

Authors:  John E Reid; Lorenz Wernisch
Journal:  Nucleic Acids Res       Date:  2011-07-23       Impact factor: 16.971

2.  Pre-replication complex proteins assemble at regions of low nucleosome occupancy within the Chinese hamster dihydrofolate reductase initiation zone.

Authors:  Yoav Lubelsky; Takayo Sasaki; Marjorie A Kuipers; Isabelle Lucas; Michelle M Le Beau; Sandra Carignon; Michelle Debatisse; Joseph A Prinz; Jonathan H Dennis; David M Gilbert
Journal:  Nucleic Acids Res       Date:  2010-12-09       Impact factor: 16.971
  2 in total

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