Correction: A comparison of peak callers used for DNase-Seq data (PLoS ONE (2014) 9, 5 (e96303) DOI: 10.1371/journal.pone.0096303);A comparison of peak callers used for DNase-Seq data

PLoS ONE

Volumn 9, Issue 5, 2014, Pages

  Koohy, Hashem ^a,b   Down, Thomas A ^a   Spivakov, Mikhail ^b   Hubbard, Tim ^a  

^a BABRAHAM INSTITUTE   (United Kingdom)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DEOXYRIBONUCLEASE; TRANSCRIPTION FACTOR; CHROMATIN;

ACCURACY; ALGORITHM; ARTICLE; BINDING AFFINITY; BINDING SITE; CELL TYPE; CONTROLLED STUDY; DATA ANALYSIS; F SEQUENCING ALGORITHM; GENE IDENTIFICATION; GENETIC ALGORITHM; GENETIC DATABASE; HIGH THROUGHPUT SEQUENCING; HOTSPOT ALGORITHM; IN VIVO STUDY; INTERMETHOD COMPARISON; MACS ALGORITHM; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; PEAK CALLING ALGORITHM; PROTEIN BINDING; QUALITY CONTROL; SENSITIVITY AND SPECIFICITY; SIGNAL DETECTION; ZINBA ALGORITHM; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DNA SEQUENCE; GENETICS; PROCEDURES;

ALGORITHMS; BINDING SITES; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DEOXYRIBONUCLEASES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; SEQUENCE ANALYSIS, DNA;

EID: 84901495997     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0105136     Document Type: Erratum

References (29)

1. Kim TH, Ren B (2006) Genome-wide analysis of protein-DNA interactions. Annual review of genomics and human genetics 7: 81-102. (Pubitemid 44627923)
2. Tong Y, Falk J (2009) Genome-wide analysis for protein-DNA interaction: ChIP-chip. Methods in molecular biology (Clifton, NJ) 590: 235-251.
3. ENCODE Project Consortium, Bernstein BE, Birney E, Dunham I, Green ED, et al. (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 488: 57-74.
4. Crawford GE, Holt IE, Whittle J, Webb BD, Tai D, et al. (2006) Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome research 16: 123-131. (Pubitemid 43048941)
5. Song L, Zhang Z, Grasfeder LL, Boyle AP, Giresi PG, et al. (2011) Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome research 21: 1757-1767.
6. Zeng W, Mortazavi A (2012) Technical considerations for functional sequencing assays. Nature Immunology 13: 802-807.
7. John S, Sabo PJ, Thurman RE, Sung MH, Biddie SC, et al. (2011) Chromatin accessibility predetermines glucocorticoid receptor binding patterns. Nature genetics: 1-7.
8. Thurman RE, Rynes E, Humbert R, Vierstra J, Maurano MT, et al. (2012) The accessible chromatin landscape of the human genome. Nature 489: 75-82.
9. Pepke S, Wold B, Mortazavi A (2009) Computation for ChIP-seq and RNA-seq studies. Nature Methods 6: S22-32.
10. Kim H, Kim J, Selby H, Gao D, Tong T, et al. (2011) A short survey of computational analysis methods in analysing ChIP-seq data. Human genomics 5: 117-123.
11. Szalkowski AM, Schmid CD (2011) Rapid innovation in ChIP-seq peak-calling algorithms is out-distancing benchmarking efforts. Briefings in Bioinformatics 12: 626-633.
12. Rye MB, Sætrom P, Drabløs F (2011) A manually curated ChIP-seq benchmark demonstrates room for improvement in current peak-finder programs. Nucleic Acids Research 39: e25.
13. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based analysis of ChIP-Seq (MACS). Genome Biology 9: R137.
14. Ramagopalan SV, Heger A, Berlanga AJ,Maugeri NJ, Lincoln MR, et al. (2010) A ChIP-seq defined genome-wide map of vitamin D receptor binding: associations with disease and evolution. Genome research 20: 1352-1360.
15. Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, et al. (2012) ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome research 22: 1813-1831.
16. Kharchenko PV, Tolstorukov MY, Park PJ (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nature biotechnology 26: 1351-1359.
17. Rashid NU, Giresi PG, Ibrahim JG, Sun W, Lieb JD (2011) ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions. Genome Biology 12: R67.
18. Baek S, Sung MH, Hager GL (2011) Quantitative analysis of genome-wide chromatin remodeling. Methods in molecular biology (Clifton, NJ) 833: 433-441.
19. Madrigal P, Krajewski P (2012) Current bioinformatic approaches to identify DNase I hypersensitive sites and genomic footprints from DNase-seq data. Frontiers in genetics 3: 230.
20. Boyle AP, Guinney J, Crawford GE, Furey TS (2008) F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics (Oxford, England) 24: 2537-2538.
21. Gaulton KJ, Nammo T, Pasquali L, Simon JM, Giresi PG, et al. (2010) A map of open chromatin in human pancreatic islets. Nature genetics 42: 255-259.
22. Wang YM, Zhou P, Wang LY, Li ZH, Zhang YN, et al. (2012) Correlation between DNase I hypersensitive site distribution and gene expression in HeLa S3 cells. PLOS ONE 7: e42414.
23. Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, et al. (2012) BEDOPS: high-performance genomic feature operations. Bioinformatics (Oxford, England) 28: 1919-1920.
24. Quinlan AR, Hall IM (2010) BEDTools: a exible suite of utilities for comparing genomic features. Bioinformatics (Oxford, England) 26: 841-842.
25. Koohy H, Down TA, Hubbard TJ (2013) Chromatin Accessibility Data Sets Show Bias Due to Sequence Specificity of the DNase I Enzyme. PloS one 8: e69853.
26. Song L, Crawford GE (2010) DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells. Cold Spring Harbor protocols 2010: pdb.prot5384.
27. Sabo PJ, Kuehn MS, Thurman R, Johnson BE, Johnson EM, et al. (2006) Genome-scale mapping of DNase I sensitivity in vivo using tiling DNA microarrays. Nature methods 3: 511-518. (Pubitemid 43941768)
28. Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, et al. (2012) DNaseI sensitivity QTLs are a major determinant of human expression variation. Nature 482: 390-394.
29. Down TA, Piipari M, Hubbard TJP (2011) Dalliance: interactive genome viewing on the web. Bioinformatics 27: 889-890.