publication . Other literature type . Article . 2016

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering

Müller, Lydia; Gerighausen, Daniel; Farman, Mariam; Zeckzer, Dirk;
  • Published: 15 Sep 2016
  • Publisher: Springer Science and Business Media LLC
  • Country: Germany
Abstract
Background Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed. Results We propose a new peak-caller called ‘Sierra Platinum’ that allows peak-calling of replicated ChIP-seq experiments. Moreover, it provides a variety of qualit...
Subjects
free text keywords: ChIP-Seq, Histonmodifikation, Replikation, ChIP-seq, Chromatin ImmunoPrecipitation DNA-Sequencing, peak-caller, histone modifications, replicate analysis, ddc:004, ddc:530, Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications, Bioinformatics, DNA microarray, Regulation of gene expression, Chip, Biology, Histone, biology.protein, Methodology Article, ChIP-seq, Peak-caller, Histone modifications, Replicate analysis
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Abstract
Background Histone modifications play an important role in gene regulation. Their genomic locations are of great interest. Usually, the location is measured by ChIP-seq and analyzed with a peak-caller. Replicated ChIP-seq experiments become more and more available. However, their analysis is based on single-experiment peak-calling or on tools like PePr which allows peak-calling of replicates but whose underlying model might not be suitable for the conditions under which the experiments are performed. Results We propose a new peak-caller called ‘Sierra Platinum’ that allows peak-calling of replicated ChIP-seq experiments. Moreover, it provides a variety of qualit...
Subjects
free text keywords: ChIP-Seq, Histonmodifikation, Replikation, ChIP-seq, Chromatin ImmunoPrecipitation DNA-Sequencing, peak-caller, histone modifications, replicate analysis, ddc:004, ddc:530, Biochemistry, Applied Mathematics, Molecular Biology, Structural Biology, Computer Science Applications, Bioinformatics, DNA microarray, Regulation of gene expression, Chip, Biology, Histone, biology.protein, Methodology Article, ChIP-seq, Peak-caller, Histone modifications, Replicate analysis
Related Organizations

Koohy, H, Down, TA, Spivakov, M, Hubbard, T. A Comparison of Peak Callers Used for DNase-Seq Data. PLoS ONE. 2014; 9 (5): 96303 [OpenAIRE] [DOI]

Wilbanks, EG, Facciotti, MT. Evaluation of Algorithm Performance in ChIP-Seq Peak Detection. PLoS ONE. 2010; 5 (7): 11471 [OpenAIRE] [DOI]

Integrative analysis of 111 reference human epigenomes. Nature. 2015; 518 (7539): 317-30 [OpenAIRE] [PubMed] [DOI]

Zhang, Y, Liu, T, Meyer, CA, Eeckhoute, J, Johnson, DS, Bernstein, BE, Nusbaum, C, Myers, RM, Brown, M, Li, W. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9 (9): 137 [OpenAIRE] [DOI]

Zhang, Y, Lin, YH, Johnson, TD, Rozek, LS, Sartor, MA. PePr: a peak-calling prioritization pipeline to identify consistent or differential peaks from replicated ChIP-Seq data. Bioinformatics. 2014; 30 (18): 2568-75 [OpenAIRE] [PubMed] [DOI]

Lun, ATL, Smyth, GK. csaw: a Bioconductor package for differential binding analysis of ChIP-seq data using sliding windows. Nucleic Acids Res. 2016; 44 (5): 45 [OpenAIRE] [PubMed] [DOI]

Robinson, MD, McCarthy, DJ, Smyth, GK. edger: a bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010; 26 (1): 139-40 [OpenAIRE] [PubMed] [DOI]

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): 389-93 [OpenAIRE] [PubMed]

Hedges, LV, Olkin, I. Statistical Methods for Meta-analysis. 1985

Meshorer, E, Misteli, T. Chromatin in pluripotent embryonic stem cells and differentiation. Nat Rev Mol Cell Biol. 2006; 7 (7): 540-6 [OpenAIRE] [PubMed] [DOI]

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publication . Other literature type . Article . 2016

Sierra platinum: a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering

Müller, Lydia; Gerighausen, Daniel; Farman, Mariam; Zeckzer, Dirk;