HiChIP: A high-throughput pipeline for integrative analysis of ChIP-Seq data

BMC Bioinformatics

Volumn 15, Issue 1, 2014, Pages

  Yan, Huihuang ^a   Evans, Jared ^a   Kalmbach, Mike ^a   Moore, Raymond ^a   Middha, Sumit ^a   Luban, Stanislav ^a,b   Wang, Liguo ^a   Bhagwate, Aditya ^a   Li, Ying ^a   Sun, Zhifu ^a   Chen, Xianfeng ^a   Kocher, Jean Pierre A ^a  

^a MAYO CLINIC   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

ChIP Seq; Duplicate filtering; Irreproducible discovery rate; Next generation sequencing; Peak calling

Indexed keywords

CHIP-SEQ; DUPLICATE FILTERING; HIGH-THROUGHPUT; INTEGRATIVE ANALYSIS; NEXT-GENERATION SEQUENCING; PEAK CALLING;

TRANSCRIPTION FACTOR;

ANIMAL; ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME MAP; COMPUTER PROGRAM; GENOMICS; HIGH THROUGHPUT SEQUENCING; HUMAN; METABOLISM; METHODOLOGY; MOLECULAR GENETICS; MOUSE; STATISTICAL ANALYSIS;

ANIMALS; BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; CHROMOSOME MAPPING; DATA INTERPRETATION, STATISTICAL; GENOMICS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; MICE; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE; TRANSCRIPTION FACTORS;

EID: 84906822160     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-15-280     Document Type: Article

References (29)

1. Furey TS. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 2012, 13(12):840-852.
2. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res 2012, 22(9):1813-1831.
3. Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6(11 Suppl):S22-S32.
4. Wilbanks EG, Facciotti MT. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One 2010, 5(7):e11471.
5. Chen Y, Negre N, Li Q, Mieczkowska JO, Slattery M, Liu T, Zhang Y, Kim TK, He HH, Zieba J, Ruan Y, Bickel PJ, Myers RM, Wold BJ, White KP, Lieb JD, Liu XS. Systematic evaluation of factors influencing ChIP-seq fidelity. Nat Methods 2012, 9(6):609-614.
6. Zang C, Schones DE, Zeng C, Cui K, Zhao K, Peng W. A clustering approach for identification of enriched domains from histone modification ChIP-Seq data. Bioinformatics 2009, 25(15):1952-1958.
7. Wang J, Lunyak VV, Jordan IK. BroadPeak: a novel algorithm for identifying broad peaks in diffuse ChIP-seq datasets. Bioinformatics 2013, 29(4):492-493.
8. Song Q, Smith AD. Identifying dispersed epigenomic domains from ChIP-Seq data. Bioinformatics (Oxford, England) 2011, 27(6):870-871.
9. Kumar V, Muratani M, Rayan NA, Kraus P, Lufkin T, Ng HH, Prabhakar S. Uniform, optimal signal processing of mapped deep-sequencing data. Nat Biotechnol 2013, 31(7):615-622.
10. Li Q, Brown JB, Huang H, Bickel PJ. Measuring reproducibility of high-throughput experiments. Ann Appl Stat 2011, 5(3):1752-1779.
11. McLean CY, Bristor D, Hiller M, Clarke SL, Schaar BT, Lowe CB, Wenger AM, Bejerano G. GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol 2010, 28(5):495-501.
12. Shin H, Liu T, Manrai AK, Liu XS. CEAS: cis-regulatory element annotation system. Bioinformatics 2009, 25(19):2605-2606.
13. Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I, Tora L. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res 2011, 39(6):e35.
14. Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, Lapointe DS, Green MR. ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 2010, 11:237.
15. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res 2009, 37(Web Server issue):W202-W208.
16. Bardet AF, He Q, Zeitlinger J, Stark A. A computational pipeline for comparative ChIP-seq analyses. Nat Protoc 2012, 7(1):45-61.
17. Boeva V, Lermine A, Barette C, Guillouf C, Barillot E. Nebula-a web-server for advanced ChIP-seq data analysis. Bioinformatics 2012, 28(19):2517-2519.
18. Mercier E, Droit A, Li L, Robertson G, Zhang X, Gottardo R. An integrated pipeline for the genome-wide analysis of transcription factor binding sites from ChIP-Seq. PLoS One 2011, 6(2):e16432.
19. Barozzi I, Termanini A, Minucci S, Natoli G. Fish the ChIPs: a pipeline for automated genomic annotation of ChIP-Seq data. Biol Direct 2011, 6:51.
20. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9(9):R137.
21. Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR, Ali S, Chin SF, Palmieri C, Caldas C, Carroll JS. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 2012, 481(7381):389-393.
22. Ptasinska A, Assi SA, Mannari D, James SR, Williamson D, Dunne J, Hoogenkamp M, Wu M, Care M, McNeill H, Cauchy P, Cullen M, Tooze RM, Tenen DG, Young BD, Cockerill PN, Westhead DR, Heidenreich O, Bonifer C. Depletion of RUNX1/ETO in t(8;21) AML cells leads to genome-wide changes in chromatin structure and transcription factor binding. Leukemia 2012, 26(8):1829-1841.
23. Lunter G, Goodson M. Stampy: a statistical algorithm for sensitive and fast mapping of Illumina sequence reads. Genome Res 2011, 21(6):936-939.
24. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009, 25(14):1754-1760.
25. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/Map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079.
26. Chung D, Kuan PF, Li B, Sanalkumar R, Liang K, Bresnick EH, Dewey C, Keles S. Discovering transcription factor binding sites in highly repetitive regions of genomes with multi-read analysis of ChIP-Seq data. PLoS Comput Biol 2011, 7(7):e1002111.
27. Robinson JT, Thorvaldsdottir H, Winckler W, Guttman M, Lander ES, Getz G, Mesirov JP. Integrative genomics viewer. Nat Biotechnol 2011, 29(1):24-26.
28. Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 2010, 26(6):841-842.
29. Carroll JS, Meyer CA, Song J, Li W, Geistlinger TR, Eeckhoute J, Brodsky AS, Keeton EK, Fertuck KC, Hall GF, Wang Q, Bekiranov S, Sementchenko V, Fox EA, Silver PA, Gingeras TR, Liu XS, Brown M. Genome-wide analysis of estrogen receptor binding sites. Nat Genet 2006, 38(11):1289-1297.