diffReps: Detecting Differential Chromatin Modification Sites from ChIP-seq Data with Biological Replicates

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Shen, Li ^a   Shao, Ning Yi ^a   Liu, Xiaochuan ^a   Maze, Ian ^b   Feng, Jian ^a   Nestler, Eric J ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b ROCKEFELLER UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALTERNATIVE RNA SPLICING; ANIMAL EXPERIMENT; ARTICLE; BRAIN REGION; CHROMATIN IMMUNOPRECIPITATION; CHROMATIN IMMUNOPRECIPITATION FOLLOWED BY DEEP SEQUENCING; CHROMATIN STRUCTURE; COMPARATIVE STUDY; COMPUTER PREDICTION; COMPUTER PROGRAM; CONTROLLED STUDY; EXON; GENE EXPRESSION; HUMAN; HUMAN CELL; INFORMATION PROCESSING; INFORMATION RETRIEVAL; MOUSE; NONHUMAN; NUCLEUS ACCUMBENS; SENSITIVITY AND SPECIFICITY; UPREGULATION;

ALGORITHMS; ANIMALS; BINDING SITES; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; COCAINE; DATA MINING; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTONES; HUMANS; MICE; NUCLEUS ACCUMBENS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE; VASOCONSTRICTOR AGENTS;

EID: 84878834064     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0065598     Document Type: Article

References (34)

1. Kidder BL, Hu G, Zhao K, (2011) ChIP-Seq: technical considerations for obtaining high-quality data. Nature immunology 12: 918-922.
2. Park PJ, (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10: 669-680.
3. Szalkowski AM, Schmid CD (2010) Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts. Briefings in Bioinformatics.
4. Liang K, Keles S, (2012) Detecting differential binding of transcription factors with ChIP-seq. Bioinformatics 28: 121-122.
5. Taslim C, Huang T, Lin S, (2011) DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models. Bioinformatics 27: 1569-1570.
6. Xu H, Wei CL, Lin F, Sung WK, (2008) An HMM approach to genome-wide identification of differential histone modification sites from ChIP-seq data. Bioinformatics 24: 2344-2349.
7. Luco RF, Allo M, Schor IE, Kornblihtt AR, Misteli T, (2011) Epigenetics in Alternative Pre-mRNA Splicing. Cell 144: 16-26.
8. Maze I, Feng J, Wilkinson MB, Sun H, Shen L, et al. (2011) Cocaine dynamically regulates heterochromatin and repetitive element unsilencing in nucleus accumbens. Proceedings of the National Academy of Sciences of the United States of America 108: 3035-3040.
9. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS biology 9: e1001046.
10. Anders S, Huber W, (2010) Differential expression analysis for sequence count data. Genome biology 11: R106.
11. Robinson MD, McCarthy DJ, Smyth GK, (2010) edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26: 139-140.
12. Xu H, Handoko L, Wei XL, Ye CP, Sheng JP, et al. (2010) A signal-noise model for significance analysis of ChIP-seq with negative control. Bioinformatics 26: 1199-1204.
13. Barski A, Cuddapah S, Cui K, Roh T-Y, Schones DE, et al. (2007) High-Resolution Profiling of Histone Methylations in the Human Genome. Cell 129: 823-837.
14. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448: 553-560.
15. Sims RJ, Millhouse S, Chen CF, Lewis BA, Erdjument-Bromage H, et al. (2007) Recognition of trimethylated histone h3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Molecular Cell 28: 665-676.
16. Trapnell C, Roberts A, Goff L, Pertea G, Kim D, et al. (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols 7: 562-578.
17. Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature biotechnology 28: 511-515.
18. Zhu LJ, Gazin C, Lawson ND, Pages H, Lin SM, et al. (2010) ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data. BMC Bioinformatics 11: 237.
19. Spitz F, Gonzalez F, Duboule D, (2003) A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113: 405-417.
20. Magklara A, Yen A, Colquitt BM, Clowney EJ, Allen W, et al. (2011) An epigenetic signature for monoallelic olfactory receptor expression. Cell 145: 555-570.
21. Warren DT, Zhang Q, Weissberg PL, Shanahan CM, (2005) Nesprins: intracellular scaffolds that maintain cell architecture and coordinate cell function? Expert reviews in molecular medicine 7: 1-15.
22. Kramer OH, (2009) HDAC2: a critical factor in health and disease. Trends in pharmacological sciences 30: 647-655.
23. Host L, Dietrich JB, Carouge D, Aunis D, Zwiller J, (2011) Cocaine self-administration alters the expression of chromatin-remodelling proteins; modulation by histone deacetylase inhibition. Journal of psychopharmacology 25: 222-229.
24. Pierce RC, Pierce-Bancroft AF, Prasad BM, (1999) Neurotrophin-3 contributes to the initiation of behavioral sensitization to cocaine by activating the Ras/Mitogen-activated protein kinase signal transduction cascade. The Journal of neuroscience: the official journal of the Society for Neuroscience 19: 8685-8695.
25. Zhang GC, Hoffmann J, Parelkar NK, Liu XY, Mao LM, et al. (2007) Cocaine increases Ras-guanine nucleotide-releasing factor 1 protein expression in the rat striatum in vivo. Neuroscience letters 427: 117-121.
26. Zhuravliova E, Barbakadze T, Narmania N, Sepashvili M, Mikeladze DG, (2009) Hypoinsulinemia alleviates the GRF1/Ras/Akt anti-apoptotic pathway and induces alterations of mitochondrial ras trafficking in neuronal cells. Neurochemical research 34: 1076-1082.
27. Fasano S, D'Antoni A, Orban PC, Valjent E, Putignano E, et al. (2009) Ras-guanine nucleotide-releasing factor 1 (Ras-GRF1) controls activation of extracellular signal-regulated kinase (ERK) signaling in the striatum and long-term behavioral responses to cocaine. Biological psychiatry 66: 758-768.
28. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, et al. (2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biology 9.
29. Di Y, Schafer Daniel W, Cumbie Jason S, Chang Jeff H, (2011) The NBP Negative Binomial Model for Assessing Differential Gene Expression from RNA-Seq. Statistical Applications in Genetics and Molecular Biology 10: 1.
30. Sokal RR, Rohlf FJ (1995) Biometry. New York: W.H. Freeman & Co.
31. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B (Methodological) 57: 289-300.
32. Rosenfeld J, Wang Z, Schones D, Zhao K, DeSalle R, et al. (2009) Determination of enriched histone modifications in non-genic portions of the human genome. BMC Genomics 10: 143.
33. Quinlan AR, Hall IM, (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26: 841-842.
34. Robinson JT, Thorvaldsdóttir H, Winckler W, Guttman M, Lander ES, et al. (2011) Integrative genomics viewer. Nature Biotechnology 29: 24-26.