The analysis of ChIP-seq data

Methods in Enzymology

Volumn 497, Issue , 2011, Pages 51-73

  Ma, Wenxiu ^a   Wong, Wing Hung ^b  

^a Stanford University   (United States)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA; RNA POLYMERASE;

ARTICLE; CHIP SEQ; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME; DNA SEQUENCE; GENE LOCUS; GENOME; HUMAN; NONHUMAN; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; QUALITY CONTROL; RNA ANALYSIS; RNA POLYMERASE TRANSCRIPTION; STATISTICAL ANALYSIS;

BASE SEQUENCE; CHROMATIN IMMUNOPRECIPITATION; COMPUTATIONAL BIOLOGY; DATABASES, NUCLEIC ACID; GENOME; HUMANS; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 79957448422     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-385075-100003-2     Document Type: Article

References (36)

1. A.P. Boyle, J. Guinney, G.E. Crawford, and T.S. Furey F-Seq: A feature density estimator for high-throughput sequence tags Bioinformatics 24 2008 2537 2538
2. J.S. Carroll, C.A. Meyer, J. Song, W. Li, T.R. Geistlinger, J. Eeckhoute, A.S. Brodsky, E.K. Keeton, K.C. Fertuck, G.F. Hall, Q. Wang, and S. Bekiranov Genome-wide analysis of estrogen receptor binding sites Nat. Genet. 38 2006 1289 1297 (Pubitemid 44646291)
3. S. Cawley, S. Bekiranov, H.H. Ng, P. Kapranov, E.A. Sekinger, D. Kampa, A. Piccolboni, V. Sementchenko, J. Cheng, A.J. Williams, R. Wheeler, and B. Wong Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs Cell 116 2004 499 509 (Pubitemid 38264428)
4. X. Chen, H. Xu, P. Yuan, F. Fang, M. Huss, V.B. Vega, E. Wong, Y.L. Orlov, W. Zhang, J. Jiang, Y.H. Loh, and H.C. Yeo Integration of external signaling pathways with the core transcriptional network in embryonic stem cells Cell 133 2008 1106 1117 (Pubitemid 351787745)
5. J.C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer Substantial biases in ultra-short read data sets from high-throughput DNA sequencing Nucleic Acids Res. 36 2008 e105
6. G.M. Euskirchen, J.S. Rozowsky, C.L. Wei, W.H. Lee, Z.D. Zhang, S. Hartman, O. Emanuelsson, V. Stolc, S. Weissman, M.B. Gerstein, Y. Ruan, and M. Snyder Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies Genome Res. 17 2007 898 909 (Pubitemid 46919724)
7. A.P. Fejes, G. Robertson, M. Bilenky, R. Varhol, M. Bainbridge, and S.J. Jones FindPeaks 3.1: A tool for identifying areas of enrichment from massively parallel short-read sequencing technology Bioinformatics 24 2008 1729 1730
8. H. Ji, S.A. Vokes, and W.H. Wong A comparative analysis of genome-wide chromatin immunoprecipitation data for mammalian transcription factors Nucleic Acids Res. 34 21 2006 e146
9. H. Ji, H. Jiang, W. Ma, D.S. Johnson, R.M. Myers, and W.H. Wong An integrated software system for analyzing ChIP-chip and ChIP-seq data Nat. Biotechnol. 26 2008 1293 1300
10. H. Jiang, and W.H. Wong SeqMap: Mapping massive amount of oligonucleotides to the genome Bioinformatics 24 2008 2395 2396
11. H. Jiang, F. Wang, N.P. Dyer, and W.H. Wong CisGenome Browser: A flexible tool for genomic data visualization Bioinformatics 26 2010 1781 1782
12. D.S. Johnson, A. Mortazavi, R.M. Myers, and B. Wold Genome-wide mapping of in vivo protein-DNA interactions Science 316 2007 1497 1502 (Pubitemid 46906620)
13. R. Jothi, S. Cuddapah, A. Barski, K. Cui, and K. Zhao Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data Nucleic Acids Res. 36 2008 5221 5231
14. P. Kapranov, S.E. Cawley, J. Drenkow, S. Bekiranov, R.L. Strausberg, S.P. Fodor, and T.R. Gingeras Large-scale transcriptional activity in chromosomes 21 and 22 Science 296 2002 916 919 (Pubitemid 34464898)
15. W.J. Kent, C.W. Sugnet, T.S. Furey, K.M. Roskin, T.H. Pringle, A.M. Zahler, and D. Haussler The human genome browser at UCSC Genome Res. 12 2002 996 1006 (Pubitemid 34662293)
16. P.V. Kharchenko, M.Y. Tolstorukov, and P.J. Park Design and analysis of ChIP-seq experiments for DNA-binding proteins Nat. Biotechnol. 26 2008 1351 1359
17. B. Langmead, C. Trapnell, M. Pop, and S.L. Salzberg Ultrafast and memory-efficient alignment of short DNA sequences to the human genome Genome Biol. 10 2009 R25
18. C.E. Lawrence, S.F. Altschul, M.S. Boguski, J.S. Liu, A.F. Neuwald, and J.C. Wootton Detecting subtle sequence signals: A Gibbs sampling strategy for multiple alignment Science 262 1993 208 214
19. H. Li, J. Ruan, and R. Durbin Mapping short DNA sequencing reads and calling variants using mapping quality scores Genome Res. 18 2008 1851 1858
20. R. Li, C. Yu, Y. Li, T.W. Lam, S.M. Yiu, K. Kristiansen, and J. Wang SOAP2: An improved ultrafast tool for short read alignment Bioinformatics 25 2009 1966 1967
21. J.S. Liu The collapsed Gibbs sampler with applications to a gene regulation problem J. Am. Stat. Assoc. 89 1994 958 966
22. M. Margulies, M. Egholm, W.E. Altman, S. Attiya, J.S. Bader, L.A. Bemben, J. Berka, M.S. Braverman, Y.J. Chen, Z. Chen, S.B. Dewell, and L. Du Genome sequencing in microfabricated high-density picolitre reactors Nature 437 2005 376 380 (Pubitemid 41613494)
23. K.J. McKernan, H.E. Peckham, G.L. Costa, S.F. McLaughlin, Y. Fu, E.F. Tsung, C.R. Clouser, C. Duncan, J.K. Ichikawa, C.C. Lee, Z. Zhang, and S.S. Ranade Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding Genome Res. 19 2009 1527 1541
24. J.W. Nicol, G.A. Helt, S.G. Blanchard Jr. , A. Raja, and A.E. Loraine The Integrated Genome Browser: Free software for distribution and exploration of genome-scale datasets Bioinformatics 25 2009 2730 2731
25. Z. Ouyang, Q. Zhou, and W.H. Wong ChIP-Seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells Proc. Natl. Acad. Sci. USA 106 2009 21521 21526
26. B. Rhead, D. Karolchik, R.M. Kuhn, A.S. Hinrichs, A.S. Zweig, P.A. Fujita, M. Diekhans, K.E. Smith, K.R. Rosenbloom, B.J. Raney, A. Pohl, and M. Pheasant The UCSC Genome Browser database: Update 2010 Nucleic Acids Res. 38 2010 D613 D619
27. G. Robertson, M. Hirst, M. Bainbridge, M. Bilenky, Y. Zhao, T. Zeng, G. Euskirchen, B. Bernier, R. Varhol, A. Delaney, N. Thiessen, and O.L. Griffith Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing Nat. Methods 4 2007 651 657 (Pubitemid 47202477)
28. J. Rozowsky, G. Euskirchen, R.K. Auerbach, Z.D. Zhang, T. Gibson, R. Bjornson, N. Carriero, M. Snyder, and M.B. Gerstein PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls Nat. Biotechnol. 27 2009 66 75
29. A. Siepel, G. Bejerano, J.S. Pedersen, A.S. Hinrichs, M. Hou, K. Rosenbloom, H. Clawson, J. Spieth, L.W. Hillier, S. Richards, G.M. Weinstock, and R.K. Wilson Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes Genome Res. 15 2005 1034 1050 (Pubitemid 41126859)
30. D.R. Smith, A.R. Quinlan, H.E. Peckham, K. Makowsky, W. Tao, B. Woolf, L. Shen, W.F. Donahue, N. Tusneem, M.P. Stromberg, D.A. Stewart, and L. Zhang Rapid whole-genome mutational profiling using next-generation sequencing technologies Genome Res. 18 2008 1638 1642
31. The ENCODE Project Consortium Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project Nature 447 2007 799 816
32. The Genome Sequencing Consortium Initial sequencing and analysis of the human genome Nature 409 2001 860 921
33. G. Tuteja, P. White, J. Schug, and K.H. Kaestner Extracting transcription factor targets from ChIP-Seq data Nucleic Acids Res. 37 2009 e113
34. A. Valouev, D.S. Johnson, A. Sundquist, C. Medina, E. Anton, S. Batzoglou, R.M. Myers, and A. Sidow Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data Nat. Methods 5 2008 829 834
35. E.D. Wederell, M. Bilenky, R. Cullum, N. Thiessen, M. Dagpinar, A. Delaney, R. Varhol, Y. Zhao, T. Zeng, B. Bernier, M. Ingham, and M. Hirst Global analysis of in vivo Foxa2-binding sites in mouse adult liver using massively parallel sequencing Nucleic Acids Res. 36 2008 4549 4564
36. Y. Zhang, T. Liu, C.A. Meyer, J. Eeckhoute, D.S. Johnson, B.E. Bernstein, C. Nussbaum, R.M. Myers, M. Brown, W. Li, and X.S. Liu Model-based analysis of ChIP-Seq (MACS) Genome Biol. 9 2008 R137