Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data.
BACKGROUND
Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is an assay used for investigating DNA-protein-binding or post-translational chromatin/histone modifications. As with all high-throughput technologies, it requires thorough bioinformatic processing of the data for which there is no standard yet. The primary goal is to reliably identify and localize genomic regions that bind a specific protein. Further investigation compares binding profiles of functionally related proteins, or binding profiles of the same proteins in different genetic backgrounds or experimental conditions. Ultimately, the goal is to gain a mechanistic understanding of the effects of DNA binding events on gene expression.


RESULTS
We present a free, open-source R/Bioconductor package Starr that facilitates comparative analysis of ChIP-chip data across experiments and across different microarray platforms. The package provides functions for data import, quality assessment, data visualization and exploration. Starr includes high-level analysis tools such as the alignment of ChIP signals along annotated features, correlation analysis of ChIP signals with complementary genomic data, peak-finding and comparative display of multiple clusters of binding profiles. It uses standard Bioconductor classes for maximum compatibility with other software. Moreover, Starr automatically updates microarray probe annotation files by a highly efficient remapping of microarray probe sequences to an arbitrary genome.


CONCLUSIONS
Starr is an R package that covers the complete ChIP-chip workflow from data processing to binding pattern detection. It focuses on the high-level data analysis, e.g., it provides methods for the integration and combined statistical analysis of binding profiles and complementary functional genomics data. Starr enables systematic assessment of binding behaviour for groups of genes that are alingned along arbitrary genomic features.
Zacher
Benedikt
B
Gene Center, Department of Chemistry and Biochemistry, Ludwig-Maximilians-University of Munich, Feodor-Lynen-Str, 25, D-81377 Munich, Germany.
Kuan
Pei Fen
PF
Tresch
Achim
A
D047369:Chromatin Immunoprecipitation / Q000379:methods*; D004247:DNA / Q000737:chemistry / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000737:chemistry; D030541:Databases, Genetic; D020869:Gene Expression Profiling; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA; D012984:Software
D004268:DNA-Binding Proteins; D004247:DNA
Bioinformatics. 2009 Jul 15;25(14):1838-40
19468055
Nat Biotechnol. 2008 Nov;26(11):1293-300
18978777
Bioinformatics. 2007 Apr 15;23(8):988-97
17387113
Genome Biol. 2004;5(2):R12
14759262
BMC Bioinformatics. 2009 Jun 30;10:204
19566918
Pac Symp Biocomput. 2008;:527-38
18229713
BMC Bioinformatics. 2007 Jun 26;8:221
17594472
Genome Biol. 2004;5(10):R80
15461798
Genomics. 2004 Mar;83(3):349-60
14986705
Biometrics. 2008 Jun;64(2):468-78
17888037
Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5
16569694
PLoS Comput Biol. 2008 Nov;4(11):e1000227
19043553
Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12457-62
16895995
Methods Enzymol. 2006;411:270-82
16939795
Bioinformatics. 2009 Sep 15;25(18):2369-75
19592393
BMC Genomics. 2008;9 Suppl 1:S20
18366610
Science. 2000 Dec 22;290(5500):2306-9
11125145
Genome Res. 2009 Mar;19(3):360-71
19124666
Bioinformatics. 2009 Apr 1;25(7):954-5
19193731
Bioinformatics. 2010 Mar 1;26(5):678-9
20089513
J Mol Biol. 2009 May 29;389(1):211-25
19371747
Pac Symp Biocomput. 2008;:515-26
18229712
Bioinformatics. 2005 Aug 15;21(16):3439-40
16082012