A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

Genome Biology

Volumn 10, Issue 12, 2009, Pages

  Lun, Desmond S ^a   Sherrid, Ashley ^b,c   Weiner, Brian ^d   Sherman, David R ^b,c   Galagan, James E ^d,e  

^a UNIVERSITY OF SOUTH AUSTRALIA   (Australia)

^b SEATTLE BIOMEDICAL RESEARCH INSTITUTE   (United States)

^c UNIVERSITY OF WASHINGTON   (United States)

^d BROAD INSTITUTE OF MIT AND HARVARD   (United States)

^e Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR;

ACCURACY; ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DATA ANALYSIS; INTERMETHOD COMPARISON; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; MATHEMATICAL PARAMETERS; MYCOBACTERIUM TUBERCULOSIS; PROTEIN MOTIF; BIOLOGY; COMPUTER PROGRAM; GENETICS; HUMAN; METABOLISM; METHODOLOGY; STATISTICS;

MYCOBACTERIUM TUBERCULOSIS;

BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; HUMANS; MYCOBACTERIUM TUBERCULOSIS; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 76249091269     PISSN: 14747596     EISSN: 1474760X     Source Type: Journal    
DOI: 10.1186/gb-2009-10-12-r142     Document Type: Article

References (34)

1. Mardis ER. ChIP-seq: welcome to the new frontier. Nat Methods 2007, 4:613-614. 10.1038/nmeth0807-613, 17664943.
2. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, Thiessen N, Griffith OL, He A, Marra M, Snyder M, Jones S. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 2007, 4:651-657. 10.1038/nmeth1068, 17558387.
3. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim T-K, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560. 10.1038/nature06008, 17603471.
4. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 2008, 5:829-834. 10.1038/nmeth.1246, 19160518.
5. Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316:1497-1502. 10.1126/science.1141319, 17540862.
6. Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJM. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 2008, 24:1729-1730. 10.1093/bioinformatics/btn305, 2638869, 18599518.
7. Zhang Y, Liu T, Meyer C, Eeckhoute J, Johnson D, Bernstein B, Nussbaum C, Myers R, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9:R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
8. Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 2008, 26:1293-1300. 10.1038/nbt.1505, 2596672, 18978777.
9. Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 2008, 36:5221-5231. 10.1093/nar/gkn488, 2532738, 18684996.
10. Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 2008, 26:1351-1359. 10.1038/nbt.1508, 2597701, 19029915.
11. Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 2008, 24:2537-2538. 10.1093/bioinformatics/btn480, 2732284, 18784119.
12. Zhang ZD, Rozowsky J, Snyder M, Chang J, Gerstein M. Modeling ChIP sequencing in silico with applications. PLoS Comput Biol 2008, 4:e1000158. 10.1371/journal.pcbi.1000158, 18725927.
13. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 2009, 27:66-75. 10.1038/nbt.1518, 19122651.
14. Tuteja G, White P, Schug J, Kaestner KH. Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res 2009, 37:e113. 10.1093/nar/gkp536, 2761252, 19553195.
15. Bulyk ML, McGuire AM, Masuda N, Church GM. A motif co-occurrence approach for genome-wide prediction of transcription-factor-binding sites in Escherichia coli. Genome Res 2004, 14:201-208. 10.1101/gr.1448004, 327095, 14762058.
16. Park H-D, Guinn KM, Harrell MI, Liao R, Voskuil MI, Tompa M, Schoolnik GK, Sherman DR. Rv3133c/dosR is a transcription factor that mediates the hypoxic response of Mycobacterium tuberculosis. Mol Microbiol 2003, 48:833-843. 10.1046/j.1365-2958.2003.03474.x, 1992516, 12694625.
17. Bishop CM. Pattern Recognition and Machine Learning. 2006, New York: Springer.
18. Hastie T, Tibshirani R, Friedman J. The Elements of Statistical Learning: Data Mining, Inference, and Prediction. 2001, New York: Springer.
19. Virbasius JV, Virbasius C, Scarpulla RC. Identity of GABP with NRF-2, a multisubunit activator of cytochrome oxidase expression, reveals a cellular role for an ETS domain activator of viral promoters. Genes Dev 1993, 7:380-392. 10.1101/gad.7.3.380, 8383622.
20. Boon C, Dick T. Mycobacterium bovis BCG response regulator essential for hypoxic dormancy. J Bacteriol 2002, 184:6760-6767. 10.1128/JB.184.24.6760-6767.2002, 135468, 12446625.
21. Dasgupta N, Kapur V, Singh KK, Das TK, Sachdeva S, Jyothisri K, Tyagi JS. Characterization of a two-component system, devR-devS, of Mycobacterium tuberculosis. Tuber Lung Dis 2000, 80:141-159. 10.1054/tuld.2000.0240, 10970762.
22. Sherman DR, Voskuil M, Schnappinger D, Liao R, Harrell MI, Schoolnik GK. Regulation of the Mycobacterium tuberculosis hypoxic response gene encoding α-crystallin. Proc Natl Acad Sci USA 2001, 98:7534-7539. 10.1073/pnas.121172498, 34703, 11416222.
23. Voskuil MI, Schnappinger D, Visconti KC, Harrell MI, Dolganov GM, Sherman DR, Schoolnik GK. Inhibition of respiration by nitric oxide induces a Mycobacterium tuberculosis dormancy program. J Exp Med 2003, 198:705-713. 10.1084/jem.20030205, 2194188, 12953092.
24. Schnappinger D, Ehrt S, Voskuil MI, Liu Y, Mangan JA, Monahan IM, Dolganov G, Efron B, Butcher PD, Nathan C, Schoolnik GK. Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: insights into the phagosomal environment. J Exp Med 2003, 198:693-704. 10.1084/jem.20030846, 2194186, 12953091.
25. Yuan Y, Crane DD, Simpson RM, Zhu Y, Hickey MJ, Sherman DR, Barry CE. The 16-kDa α-crystallin (Acr) protein of Mycobacterium tuberculosis is required for growth in macrophages. Proc Natl Acad Sci USA 1998, 95:9578-9583. 10.1073/pnas.95.16.9578, 21381, 9689123.
26. Shi L, Sohaskey CD, Kana BD, Dawes S, North RJ, Mizrahi V, Gennaro ML. Changes in energy metabolism of Mycobacterium tuberculosis in mouse lung and under in vitro conditions affecting aerobic respiration. Proc Natl Acad Sci USA 2005, 102:15629-15634. 10.1073/pnas.0507850102, 1255738, 16227431.
27. Yang Z-F, Mott S, Rosmarin AG. The Ets transcription factor GABP is required for cell-cycle progression. Nat Cell Biol 2007, 9:339-346. 10.1038/ncb1548, 17277770.
28. 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, 103:12457-12462. 10.1073/pnas.0601180103, 1567901, 16895995.
29. Song JS, Johnson WE, Zhu X, Zhang X, Li W, Manrai AK, Liu JS, Chen R, Liu XS. Model-based analysis of two-color arrays (MA2C). Genome Biol 2007, 8:R178. 10.1186/gb-2007-8-8-r178, 2375008, 17727723.
30. Bailey TL, Williams N, Misleh C, Li WW. MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Res 2006, 34:W369-W373. 10.1093/nar/gkl198, 1538909, 16845028.
31. Bailey TL, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 1998, 14:48-54. 10.1093/bioinformatics/14.1.48, 9520501.
32. Takai D, Jones PA. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 2002, 99:3740-3745. 10.1073/pnas.052410099, 122594, 11891299.
33. Bertsekas DP. Nonlinear Programming 1999, Belmont, MA: Athena Scientific, 2.
34. CSDeconv. , http://www.unisa.edu.au/maths/phenomics/csdeconv/