Comparison of four CHIP-Seq analytical algorithms using rice endosperm H3K27 trimethylation profiling data

PLoS ONE

Volumn 6, Issue 9, 2011, Pages

  Malone, Brandon M ^a,b   Tan, Feng ^b   Bridges, Susan M ^a,b   Peng, Zhaohua ^b  

^a MISSISSIPPI STATE UNIVERSITY   (United States)

^b MISSISSIPPI STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTONE H3; LYSINE; HISTONE;

ACCURACY; ANALYTICAL PARAMETERS; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA SEQUENCE; ENDOSPERM; GENE EXPRESSION; GENE REPRESSION; GENETIC ALGORITHM; GENETIC ASSOCIATION; HIGH THROUGHPUT SEQUENCING; HISTONE METHYLATION; INTERMETHOD COMPARISON; NONHUMAN; PLANT GENE; PLANT GENOME; PLANT METABOLISM; PREDICTION; RICE; SIGNAL TRANSDUCTION; VALIDATION STUDY; ALGORITHM; DNA METHYLATION; GENETICS;

ALGORITHMS; CHROMATIN IMMUNOPRECIPITATION; DNA METHYLATION; ENDOSPERM; HISTONES; ORYZA SATIVA; SEQUENCE ANALYSIS, DNA;

EID: 80053599512     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0025260     Document Type: Article

References (38)

1. Nix DA, Courdy SJ, Boucher KM, (2008) Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 9: 523.
2. Barski A, Cuddapah S, Cui K, Roh T, Schones D, et al. (2007) High-resolution profiling of histone methylations in the human genome. Cell 129: 823-837.
3. Boyle AP, Guinney J, Crawford GE, Furey TS, (2008) F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 24: 2537-2538.
4. Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, et al. (2008) FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 24: 1729-1730.
5. Kharchenko PV, Tolstorukov MY, Park PJ, (2008) Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 26: 1351-1359.
6. Li H, Durbin R, (2008) Maq: Mapping and Assembly with Qualities.
7. Nix DA, Courdy SJ, Boucher KM, (2008) Empirical methods for controlling false positives and estimating confidence in chIP-seq peaks. BMC Bioinformatics 9: 523.
8. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, et al. (2009) PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotech 27: 66-75.
9. Schmid C, Bucher P, (2007) ChIP-Seq Data Reveal Nucleosome Architecture of Human Promoters. Cell 131: 831-832.
10. Zhang Y, Liu T, Meyer C, Eeckhoute J, Johnson D, et al. (2008) Model-based Analysis of ChIP-Seq (MACS). Genome Biol 9: R137.
11. Zhang Y, Shin H, Song J, Lei Y, Liu XS, (2008) Identifying Positioned Nucleosomes with Epigenetic Marks in Human from ChIP-Seq. BMC Genomics 9: 537.
12. Pepke S, Wold B, Mortazavi A, (2009) Computation for ChIP-seq and RNA-seq studies. Nat Meth 6: S22-S32.
13. Barski A, Zhao K, (2009) Genomic Location Analysis by ChIP-Seq. Journal of Cellular Biochemistry 107: 11-18.
14. Zhang X, Clarenz O, Cokus S, Bernatavichute YV, Pellegrini M, et al. (2007) Whole-genome analysis of histone H3 lysine 27 trimethylation in Arabidopsis. PLoS Biol 5: e129.
15. Pien S, Grossniklaus U, (2007) Polycomb group and trithorax group proteins in Arabidopsis. Biochim Biophys Acta 1769: 375-382.
16. Lee TI, Jenner RG, Boyer LA, Guenther MG, Levine SS, et al. (2006) Control of developmental regulators by Polycomb in human embryonic stem cells. Cell 125: 301-313.
17. Boyer LA, Plath K, Zeitlinger J, Brambrink T, Medeiros LA, et al. (2006) Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature 441: 349-353.
18. Tolhuis B, de Wit E, Muijrers I, Teunissen H, Talhout W, et al. (2006) Genome-wide profiling of PRC1 and PRC2 Polycomb chromatin binding in Drosophila melanogaster. Nat Genet 38: 694-699.
19. Gehring M, Choi Y, Fischer RL, (2004) Imprinting and seed development. Plant Cell 16 (Suppl): S203-213.
20. Huh JH, Bauer MJ, Hsieh TF, Fischer R, (2007) Endosperm gene imprinting and seed development. Curr Opin Genet Dev 17: 480-485.
21. Gehring M, Huh JH, Hsieh TF, Penterman J, Choi Y, et al. (2006) DEMETER DNA glycosylase establishes MEDEA polycomb gene self-imprinting by allele-specific demethylation. Cell 124: 495-506.
22. Jullien PE, Katz A, Oliva M, Ohad N, Berger F, (2006) Polycomb group complexes self-regulate imprinting of the Polycomb group gene MEDEA in Arabidopsis. Curr Biol 16: 486-492.
23. Baroux C, Gagliardini V, Page DR, Grossniklaus U, (2006) Dynamic regulatory interactions of Polycomb group genes: MEDEA autoregulation is required for imprinted gene expression in Arabidopsis. Genes Dev 20: 1081-1086.
24. Kohler C, Page DR, Gagliardini V, Grossniklaus U, (2005) The Arabidopsis thaliana MEDEA Polycomb group protein controls expression of PHERES1 by parental imprinting. Nat Genet 37: 28-30.
25. Makarevich G, Leroy O, Akinci U, Schubert D, Clarenz O, et al. (2006) Different Polycomb group complexes regulate common target genes in Arabidopsis. EMBO Rep 7: 947-952.
26. He GM, Zhu XP, Elling AA, Chen LB, Wang XF, et al. (2010) Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids. Plant Cell 22: 17-33.
27. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25: 25-29.
28. Jiang H, Wong WH, (2008) SeqMap: mapping massive amount of oligonucleotides to the genome. Bioinformatics 24: 2395-2396.
29. Ouyang S, Zhu W, Hamilton J, Lin H, Campbell M, et al. (2007) The TIGR Rice Genome Annotation Resource: improvements and new features. Nucleic Acids Res 35: D883-887.
30. Stein LD, Mungall C, Shu S, Caudy M, Mangone M, et al. (2002) The generic genome browser: a building block for a model organism system database. Genome Res 12: 1599-1610.
31. Du Z, Zhou X, Ling Y, Zhang Z, Su Z, (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucl Acids Res 38: W64-W70.
32. Gendrel AV, Lippman Z, Martienssen R, Colot V, (2005) Profiling histone modification patterns in plants using genomic tiling microarrays. Nature Methods 2: 213-218.
33. Cox A, (2001) ELAND: Efficient Local Alignment of Nucleotide Data (unpublished).
34. Papoulis A, (1984) Conditional Probabilities and Independent Sets. Probability, Random Variables, and Stochastic Processes New York McGraw-Hill pp. 33-45.
35. Feller W, (1968) The Hypergeometric Series. An Introduction to Probability Theory and Its Applications. 3 ed New York Wiley.
36. R Development Core Team (2006) R: A Language and Environment for Statistical Computing Vienna, Austria.
37. Benjamini Y, Yekutieli D, (2001) The control of the false discovery rate in multiple tesing under dependency. Ann Stat pp. 29-1165.
38. Sequencing Project International Rice G (2005) The map-based sequence of the rice genome. Nature 436: 793-800.