An effective statistical evaluation of chipseq dataset similarity

Bioinformatics

Volumn 28, Issue 5, 2012, Pages 607-613

  Chikina, Maria D ^a   Troyanskaya, Olga G ^b  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b PRINCETON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CHROMATIN IMMUNOPRECIPITATION; COMPUTER LANGUAGE; DNA SEQUENCE; GENETIC TRANSCRIPTION; GENOMICS; METHODOLOGY;

ALGORITHMS; CHROMATIN IMMUNOPRECIPITATION; GENOMICS; PROGRAMMING LANGUAGES; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION, GENETIC;

EID: 84857822152     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts009     Document Type: Article

References (26)

1. Carstensen,L. et al. (2010) Multivariate Hawkes process models of the occurrence of regulatory elements. BMC Bioinformatics, 11, 456.
2. Chen,X. et al. (2008) Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell, 133, 1106-1117.
3. Cuddapah,S. et al. (2009) Global analysis of the insulator binding protein ctcf in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res., 19, 24-32.
4. Fu,A.Q. and Adryan,B. (2009) Scoring overlapping and adjacent signals from genomewide chip and damid assays. Mol. Biosyst., 5, 1429-1438.
5. Guttman,M. et al. (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458, 223-227.
6. Hoffman,B.G. et al. (2010) Locus co-occupancy, nucleosome positioning, and h3k4me1 regulate the functionality of foxa2-, hnf4a-, and pdx1-bound loci in islets and liver. Genome Res., 20, 1037-1051.
7. Huen,D.S. and Russell,S. (2010) On the use of resampling tests for evaluating statistical significance of binding-site co-occurrence. BMC Bioinformatics, 11, 359.
8. Janknecht,R. and Hunter,T. (1996) Versatile molecular glue. transcriptional control. Curr. Biol., 6, 951-954.
9. Johnson,D.S. et al. (2007) Genome-wide mapping of in vivo protein-dna interactions. Science, 316, 1497-1502.
10. Kunisato,A. et al. (2010) Generation of induced pluripotent stem cells by efficient reprogramming of adult bone marrow cells. Stem Cells Dev., 19, 229-238.
11. Leung,J.Y. et al. (2008) A role for Myc in facilitating transcription activation by e2f1. Oncogene, 27, 4172-4179.
12. Mikkelsen,T.S. et al. (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448, 553-560.
13. Ouyang,Z. et al. (2009) Chip-seq of transcription factors predicts absolute and differential gene expression in embryonic stem cells. Proc. Natl Acad. Sci. USA, 106, 21521-21526.
14. Pan,G. and Thomson,J.A. (2007) Nanog and transcriptional networks in embryonic stem cell pluripotency. Cell Res., 17, 42-49.
15. Park,P.J. (2009) Chip-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet., 10, 669-680.
16. Pepke,S. et al. (2009) Computation for chip-seq and rna-seq studies. Nat. Methods, 6 (11 Suppl.), S22-S32.
17. Rugg-Gunn,P.J. et al. (2010) Distinct histone modifications in stem cell lines and tissue lineages from the early mouse embryo. Proc. Natl Acad. Sci. USA, 107, 10783-10790.
18. Singh,A.M. and Dalton,S. (2009) The cell cycle and Myc intersect with mechanisms that regulate pluripotency and reprogramming. Cell Stem Cell, 5, 141-149.
19. Suzuki,A. et al. (2006) Nanog binds to smad1 and blocks bone morphogenetic proteininduced differentiation of embryonic stem cells. Proc. Natl Acad. Sci. USA, 103, 10294-10299.
20. Teytelman,L. et al. (2009) Impact of chromatin structures on dna processing for genomic analyses. PLoS One, 4, e6700.
21. Wang,J. et al. (2006) A protein interaction network for pluripotency of embryonic stem cells. Nature, 444, 364-368.
22. Wederell,E.D. et al. (2008) Global analysis of in vivo foxa2-binding sites in mouse adult liver using massively parallel sequencing. Nucleic Acids Res., 36, 4549-4564.
23. Wernig,M. et al. (2007) In vitro reprogramming of fibroblasts into a pluripotent es-celllike state. Nature, 448, 318-324.
24. Wu,W. et al. (2011) Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. Genome Res., 21, 1659-1671.
25. Zajac-Kaye,M. (2001) Myc oncogene: a key component in cell cycle regulation and its implication for lung cancer. Lung Cancer, 34 (Suppl. 2), S43-S46.
26. Zhang,Z.D. et al. (2007) Statistical analysis of the genomic distribution and correlation of regulatory elements in the encode regions. Genome Res., 17, 787-797.