HAT: Hypergeometric Analysis of Tiling-arrays with application to promoter-GeneChip data

BMC Bioinformatics

Volumn 11, Issue , 2010, Pages

  Taskesen, Erdogan ^a,b   Beekman, Renee ^a   de Ridder, Jeroen ^b,c,d   Wouters, Bas J ^a   Peeters, Justine K ^a   Touw, Ivo P ^a   Reinders, Marcel J T ^b,c   Delwel, Ruud ^a  

^a ERASMUS MEDICAL CENTER   (Netherlands)

^b DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^c NETHERLANDS BIOINFORMATICS CENTRE   (Netherlands)

^d NETHERLANDS CANCER INSTITUTE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL RESEARCH; CHROMATIN IMMUNOPRECIPITATION; INSERTIONAL MUTAGENESIS; METHOD COMPARISON; REGION OF INTEREST; REGIONS OF INTEREST; SIGNAL INTENSITIES; SIGNIFICANCE LEVELS;

GENES;

PROBES;

ARTICLE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER PROGRAM; DNA MICROARRAY; GENOME; GENOMICS; METHODOLOGY; PROMOTER REGION;

CHROMATIN IMMUNOPRECIPITATION; GENOME; GENOMICS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; SOFTWARE;

EID: 77952465822     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-11-275     Document Type: Article

References (26)

1. Aparicio O, Geisberg JV, Struhl K. Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo. Curr Protoc Cell Biol 2004, Chapter 17:Unit 17.7.
2. Liu XS. Getting started in tiling microarray analysis. PLoS Comput Biol 2007, 3(10):1842-1844. 10.1371/journal.pcbi.0030183, 2041964, 17967045.
3. Weber M, Davies JJ, Wittig D, Oakeley EJ, Haase M, Lam WL, Schübeler D. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet 2005, 37(8):853-862. 10.1038/ng1598, 16007088.
4. Bertone P, Stolc V, Royce TE, Rozowsky JS, Urban AE, Zhu X, Rinn JL, Tongprasit W, Samanta M, Weissman S, Gerstein M, Snyder M. Global identification of human transcribed sequences with genome tiling arrays. Science 2004, 306(5705):2242-2246. 10.1126/science.1103388, 15539566.
5. Crawford GE, Davis S, Scacheri PC, Renaud G, Halawi MJ, Erdos MR, Green R, Meltzer PS, Wolfsberg TG, Collins FS. DNase-chip: a high-resolution method to identify DNase I hypersensitive sites using tiled microarrays. Nat Methods 2006, 3(7):503-509. 10.1038/nmeth888, 2698431, 16791207.
6. Heidenblad M, Lindgren D, Jonson T, Liedberg F, Veerla S, Chebil G, Gudjonsson S, Borg A, Månsson W, Höglund M. Tiling resolution array CGH and high density expression profiling of urothelial carcinomas delineate genomic amplicons and candidate target genes specific for advanced tumors. BMC Med Genomics 2008, 1:3. 10.1186/1755-8794-1-3, 2227947, 18237450.
7. Royce TE, Rozowsky JS, Bertone P, Samanta M, Stolc V, Weissman S, Snyder M, Gerstein M. Issues in the analysis of oligonucleotide tiling microarrays for transcript mapping. Trends Genet 2005, 21(8):466-475. 10.1016/j.tig.2005.06.007, 1855044, 15979196.
8. Keleş S, Laan MJ, Dudoit S, Cawley SE. Multiple testing methods for ChIP-Chip high density oligonucleotide array data. J Comput Biol 2006, 13(3):579-613. 10.1089/cmb.2006.13.579, 16706714.
9. Li W, Meyer CA, Liu XS. A hidden Markov model for analyzing ChIP-chip experiments on genome tiling arrays and its application to p53 binding sequences. Bioinformatics 2005, 21(Suppl 1):i274-i282. 10.1093/bioinformatics/bti1046, 15961467.
10. Ji H, Wong WH. TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics 2005, 21(18):3629-3636. 10.1093/bioinformatics/bti593, 16046496.
11. Johnson WE, Li W, Meyer CA, Gottardo R, Carroll JS, Brown M, Liu XS. Model-based analysis of tiling-arrays for ChIP-chip. Proc Natl Acad Sci USA 2006, 103(33):12457-12462. 10.1073/pnas.0601180103, 1567901, 16895995.
12. Sun W, Buck MJ, Patel M, Davis IJ. Improved ChIP-chip analysis by a mixture model approach. BMC Bioinformatics 2009, 10:173. 10.1186/1471-2105-10-173, 2700807, 19500407.
13. Kuan PF, Chun H, Keleş S. CMARRT: a tool for the analysis of ChIP-chip data from tiling arrays by incorporating the correlation structure. Pac Symp Biocomput 2008, 515-526. 2862456, 18229712.
14. Zacher B, Kuan PF, Tresch A. Starr: Simple Tiling ARRay analysis of Affymetrix ChIP-chip data. BMC Bioinformatics 2010, 11:194. 10.1186/1471-2105-11-194, 2868012, 20398407.
15. Toedling J, Skylar O, Sklyar O, Krueger T, Fischer JJ, Sperling S, Huber W. Ringo-an R/Bioconductor package for analyzing ChIP-chip readouts. BMC Bioinformatics 2007, 8:221. 10.1186/1471-2105-8-221, 1906858, 17594472.
16. Ji X, Li W, Song J, Wei L, Liu XS. CEAS: cis-regulatory element annotation system. Nucleic Acids Res 2006, (34 Web Server):W551-W554. 10.1093/nar/gkl322, 1538818, 16845068.
17. Tinel M, Berson A, Elkahwaji J, Cresteil T, Beaune P, Pessayre D. Downregulation of cytochromes P450 in growth-stimulated rat hepatocytes: role of c-Myc induction and impaired C/EBP binding to DNA. J Hepatol 2003, 39(2):171-178. 10.1016/S0168-8278(03)00238-1, 12873812.
18. Ramji DP, Foka P. CCAAT/enhancer-binding proteins: structure, function and regulation. Biochem J 2002, 365(Pt 3):561-575. 1222736, 12006103.
19. Wang W, Wang X, Ward AC, Touw IP, Friedman AD. C/EBPalpha and G-CSF receptor signals cooperate to induce the myeloperoxidase and neutrophil elastase genes. Leukemia 2001, 15(5):779-786. 10.1038/sj.leu.2402094, 11368439.
20. Zhang P, Iwama A, Datta MW, Darlington GJ, Link DC, Tenen DG. Upregulation of interleukin 6 and granulocyte colony-stimulating factor receptors by transcription factor CCAAT enhancer binding protein alpha (C/EBP alpha) is critical for granulopoiesis. J Exp Med 1998, 188(6):1173-1184. 10.1084/jem.188.6.1173, 2212540, 9743535.
21. Erkeland SJ, Valkhof M, Heijmans-Antonissen C, van Hoven-Beijen A, Delwel R, Hermans MHA, Touw IP. Large-scale identification of disease genes involved in acute myeloid leukemia. J Virol 2004, 78(4):1971-1980. 10.1128/JVI.78.4.1971-1980.2004, 369447, 14747562.
22. Touw IP, Erkeland SJ. Retroviral insertion mutagenesis in mice as a comparative oncogenomics tool to identify disease genes in human leukemia. Mol Ther 2007, 15:13-19. 10.1038/sj.mt.6300040, 17164770.
23. Theodorou V, Kimm MA, Boer M, Wessels L, Theelen W, Jonkers J, Hilkens J. MMTV insertional mutagenesis identifies genes, gene families and pathways involved in mammary cancer. Nat Genet 2007, 39(6):759-769. 10.1038/ng2034, 17468756.
24. Suzuki T, Shen H, Akagi K, Morse HC, Malley JD, Naiman DQ, Jenkins NA, Copeland NG. New genes involved in cancer identified by retroviral tagging. Nat Genet 2002, 32:166-174. 10.1038/ng949, 12185365.
25. Mockler TC, Chan S, Sundaresan A, Chen H, Jacobsen SE, Ecker JR. Applications of DNA tiling arrays for whole-genome analysis. Genomics 2005, 85:1-15. 10.1016/j.ygeno.2004.10.005, 15607417.
26. Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003, 19(2):185-193. 10.1093/bioinformatics/19.2.185, 12538238.