Analysis of affymetrix ChiP-chip data using starr and R/Bioconductor

Cold Spring Harbor Protocols

Volumn 6, Issue 5, 2011, Pages

  Zacher, Benedikt ^a   Torkler, Phillipp ^a   Tresch, Achim ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTIC METHOD; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER PROGRAM; GENE EXPRESSION; INTERNET; MOLECULAR PROBE; PROTEIN DNA BINDING; QUALITY CONTROL; QUANTITATIVE ANALYSIS;

EID: 79957543666     PISSN: None     EISSN: 15596095     Source Type: Journal    
DOI: 10.1101/pdb.top110     Document Type: Article

References (23)

1. Bembom O, Keles S, van der Laan MJ. 2007. Supervised detection of conserved motifs in DNA sequences with cosmo. Stat Appl Genet Mol Biol, 6: Article8. http://works.bepress.com/bembom/16.
2. Chung HR, Vingron M. 2009. Comparison of sequence-dependent tiling array normalization approaches. BMC Bioinformatics 10: 204. doi: 10.1186/1471-2105-10-204.[Medline]
3. David L, Huber W, Granovskaia M, Toedling J, Palm CJ, Bofkin L, Jones T, Davis RW, Steinmetz LM. 2006. A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci 103: 5320-5325.[Abstract/Free Full Text]
4. Dengl S, Mayer A, Sun M, Cramer P. 2009. Structure and in vivo requirement of the yeast Spt6 SH2 domain. J Mol Biol 389: 211-225.[Medline]
5. Fasold M, Stadler PF, Binder H. 2010. G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration. BMC Bioinformatics 11: 207. doi: 10.1186/1471-2105-11-207.[Medline]
6. Gilbert D, Rechtsteiner A. 2009. Comments on sequence normalization of tiling array expression. Bioinformatics 25: 2171-2173.[Abstract/Free Full Text]
7. Gottardo R, Li W, Johnson WE, Liu XS. 2008. A flexible and powerful bayesian hierarchical model for ChIP-Chip experiments. Biometrics 64: 468-478.[Medline]
8. Huber W, Heydebreck A, Sueltmann H, Poustka A, Vingron M. 2002. Variance stabilization applied to microarray data calibration and to the quantification of differential expression. Bioinformatics 18: 96-104.
9. Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. 2006. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci 103: 12457-12462.[Abstract/Free Full Text]
10. Karolchik D, Hinrichs AS, Kent WJ. 2007. The UCSC Genome Browser. Curr Protoc Bioinformatics 1: 1.4. doi: 10.1002/0471250953.bi0104s28.
11. Kuan PF, Chun H, Keles S. 2008. CMARRT: A tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure. Pac Symp Biocomput. reffpage>515-526.
12. Langmead B, Trapnell C, Pop M, Salzberg SL. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10: R25. doi: 10.1186/gb-2009-10-3-r25.[Medline]
13. Parkinson H, Kapushesky M, Kolesnikov N, Rustici G, Shojatalab M, Abeygunawardena N, Berube H, Dylag M, Eman I, Farne A, et al. 2008. ArrayExpress update-from an archive of functional genomics experiments to the atlas of gene expression. Nucl. Acids Res 37: D868-D872.[Medline]
14. Scacheri PC, Crawford GE, Davis S. 2006. Statistics for ChIP-chip and DNase hypersensitivity experiments on NimbleGen arrays. Methods Enzymol 411: 270-282.[Medline]
15. Schmidberger M. 2009. Parallel Computing for Biological Data. Dissertation, LMU München: Fakultät für Mathematik, Informatik und Statistik, München.
16. Schmidberger M, Mansmann U. 2009. Parallel computing with the R language in a supercomputing environment. In High Performance Computing in Science and Engineering (ed. Wagner S, et al.), pp. 769-780. Garching, Springer.
17. Schmidberger M, Vicedo E, Mansmann U. 2009. affyPara-a bioconductor package for parallelized preprocessing algorithms of Affymetrix microarray data. Bioinform Biol Insights 3: 83-87.[Medline]
18. Siebert M, Lidschreiber M, Holger H, Söding J. 2010. A guideline for ChIP-Chip data quality control and normalization. http://www.epigenome-noe.net/www/researchtools/pdfs/p47.pdf.
19. Straub T. 2009. Basic analysis of NimbleGen ChIP-on-chip data using Bioconductor/R. http://www.epigenome-noe.net/www/researchtools/protocol.php?protid=43.
20. Toedling J, Skylar O, Krueger T, Fischer JJ, Sperling S, Huber W. 2007. Ringo-an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics 8: 221. doi: 10.1186/1471-2105-8-221.[Medline]
21. Venters BJ, Pugh BF. 2009. A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome. Genome Res. 19: 360-371.[Abstract/Free Full Text]
22. Zacher B, Kuan PF, Tresch. 2010. Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. BMC Bioinformatics 11: 194. doi: 10.1186/1471-2105-11-194.[Medline]
23. Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS, Green MR. 2010. ChIPpeakAnno: A Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 11: 237. doi: 10.1186/1471-2105-11-237.[Medline]