Tiling array data analysis: A multiscale approach using wavelets

BMC Bioinformatics

Volumn 12, Issue , 2011, Pages

  Karpikov, Alexander ^a   Rozowsky, Joel ^a   Gerstein, Mark ^a  

^a YALE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL ACTIVITY; HISTONE MODIFICATION; LOG-NORMAL DISTRIBUTION; MULTI-SCALE APPROACHES; THRESHOLDING PROCEDURES; WAVELET BASIS FUNCTIONS; WAVELET COEFFICIENTS; WAVELET TRANSFORMATIONS;

SIGNAL PROCESSING;

EXPERIMENTS;

ALGORITHM; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; DNA MICROARRAY; METHODOLOGY; WAVELET ANALYSIS;

ALGORITHMS; CHROMATIN IMMUNOPRECIPITATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; WAVELET ANALYSIS;

EID: 79951704286     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-57     Document Type: Article

References (19)

1. Yazaki J, Gregory BD, Ecker JR. Mapping the genome landscape using tiling array technology. Curr Opin Plant Biol 2007, 10(5):534-542. 10.1016/j.pbi.2007.07.006, 2665186, 17703988.
2. Bertone P, Gerstein M, Snyder M. Applications of DNA tiling arrays to experimental genome annotation and regulatory pathway discovery. Chromosome Res 2005, 13(3):259-274. 10.1007/s10577-005-2165-0, 15868420.
3. Buck MJ, Lieb JD. ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 2004, 83(3):349-360. 10.1016/j.ygeno.2003.11.004, 14986705.
4. Quackenbush J. Microarray data normalization and transformation. Nat Genet 2002, 32:496-501. 10.1038/ng1032, 12454644.
5. Johnson DS, Li W, Gordon DB, Bhattacharjee A, Curry B, Ghosh J, Brizuela L, Carroll JS, Brown M, Flicek P, et al. Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets. Genome Res 2008, 18(3):393-403. 10.1101/gr.7080508, 2259103, 18258921.
6. Lucas I, Palakodeti A, Jiang YW, Young DJ, Jiang N, Fernald AA, Le Beau MM. High-throughput mapping of origins of replication in human cells. Embo Rep 2007, 8(8):770-777. 10.1038/sj.embor.7401026, 1978075, 17668008.
7. Splitter algorithm. , http://zlab.bu.edu/splitter
8. Song JS, Johnson WE, Zhu XP, Zhang XM, Li W, Manrai AK, Liu JS, Chen RS, Liu XS. Model-based analysis of two-color arrays (MA2C). Genome Biol 2007, 8(8). 10.1186/gb-2007-8-8-r178, 2375008, 17727723.
9. Zheng M, Barrera LO, Ren B, Wu YN. ChIP-chip: Data, model, and analysis. Biometrics 2007, 63(3):787-796. 10.1111/j.1541-0420.2007.00768.x, 17825010.
10. Ozsolak F, Song JS, Liu XS, Fisher DE. High-throughput mapping of the chromatin structure of human promoters. Nature Biotechnology 2007, 25(2):244-248. 10.1038/nbt1279, 17220878.
11. Daubechies Ten lectures on wavelets: Society for Industrial and Applied Mathematics, Philadelphia, Pa 1992, Daubechies.
12. Mallat SG. A Theory for Multiresolution Signal Decomposition - the Wavelet Representation. Ieee T Pattern Anal 1989, 11(7):674-693.
13. Mathworks Wavelet Toolbox User Guide 2008, Mathworks.
14. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447(7146):799-816. 10.1038/nature05874, 2212820, 17571346.
15. Lian Z, Karpikov A, Lian J, Mahajan MC, Hartman S, Gerstein M, Snyder M, Weissman SM. A genomic analysis of RNA polymerase II modification and chromatin architecture related to 3' end RNA polyadenylation. Genome Res 2008, 18(8):1224-1237. 10.1101/gr.075804.107, 2493437, 18487515.
16. Limpert E, Stahel WA, Abbt M. Log-normal distributions across the sciences: Keys and clues. Bioscience 2001, 51(5):341-352.
17. Mutch SA, Fujimoto BS, Kuyper CL, Kuo JS, Bajjalieh SM, Chiu DT. Deconvolving single-molecule intensity distributions for quantitative microscopy measurements. Biophys J 2007, 92(8):2926-2943. 10.1529/biophysj.106.101428, 1831712, 17259276.
18. Bieda M, Xu XQ, Singer MA, Green R, Farnham PJ. Unbiased location analysis of E2F1-binding sites suggests a widespread role for E2F1 in the human genome. Genome Res 2006, 16(5):595-605. 10.1101/gr.4887606, 1457046, 16606705.
19. Euskirchen GM, Rozowsky JS, Wei CL, Lee WH, Zhang ZDD, Hartman S, Emanuelsson O, Stolc V, Weissman S, Gerstein MB, et al. Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies. Genome Res 2007, 17(6):898-909. 10.1101/gr.5583007, 1891348, 17568005.