Application of the simple and efficient Mpeak modeling in binding peak identification in ChIP-chip studies

Methods in Molecular Biology

Volumn 1067, Issue , 2013, Pages 185-202

  Zheng, Ming ^a   Li, Yunmin ^b   Lau, Yun Fai Chris ^b  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

ChIP chip; Mpeak modeling; Peak identification; SRY targets

Indexed keywords

NUCLEAR PROTEIN; TRANSCRIPTION FACTOR;

ARTICLE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DNA BINDING; GENE; GENE IDENTIFICATION; GENOME; GONAD; HYBRIDIZATION; MICROARRAY ANALYSIS; MOLECULAR MODEL; NONHUMAN; PRIORITY JOURNAL; SEX DETERMINATION; SRY GENE;

ANIMALS; BINDING SITES; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; GENES; GENOMICS; HUMANS; MICE; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PROMOTER REGIONS, GENETIC; SEX-DETERMINING REGION Y PROTEIN; SOFTWARE;

EID: 84884172764     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-607-8_12     Document Type: Article

References (32)

1. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J et al (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921
2. Gonzaga-Jauregui C, Lupski JR, Gibbs RA (2012) Human genome sequencing in health and disease. Annu Rev Med 63: 35-61
3. Chang HW, Chuang LY, Tsai MT, Yang CH (2012) The importance of integrating SNP and cheminformatics resources to pharmacogenomics. Curr Drug Metab 13: 991-999
4. Reyes A, Semenkovich NP, Whiteson K, Rohwer F, Gordon JI (2012) Going viral: next-generation sequencing applied to phage populations in the human gut. Nat Rev Microbiol 10: 607-617
5. Luciani F, Bull RA, Lloyd AR (2012) Next generation deep sequencing and vaccine design: today and tomorrow. Trends Biotechnol 30: 443-452
6. Rizzi E, Lari M, Gigli E, De Bellis G, Caramelli D (2012) Ancient DNA studies: new perspectives on old samples. Genet Sel Evol 44: 21
7. Shokralla S, Spall JL, Gibson JF, Hajibabaei M (2012) Next-generation sequencing technologies for environmental DNA research. Mol Ecol 21: 1794-1805
8. Casals F, Idaghdour Y, Hussin J, Awadalla P (2012) Next-generation sequencing approaches for genetic mapping of complex diseases. J Neuroimmunol 248: 10-22
9. Paux E, Sourdille P, Mackay I, Feuillet C (2012) Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 30: 1071-1088
10. Mueller TF, Mas VR (2012) Microarray applications in nephrology with special focus on transplantation. J Nephrol 25: 589-602
11. Lucas SM, Heath EI (2012) Current challenges in development of differentially expressed and prognostic prostate cancer biomarkers. Prostate Cancer 2012: 640968
12. Kuhn RM, Haussler D, Kent WJ (2013) The UCSC genome browser and associated tools. Brief Bioinform 14(2): 144-161, Epub ahead of print
13. da Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57
14. Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P et al (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res 15(10): 1451-1455
15. Liu T, Ortiz JA, Taing L, Meyer CA, Lee B, Zhang Y et al (2011) Cistrome: an integrative platform for transcriptional regulation studies. Genome Biol 12: R83
16. Kim TH, Ren B (2006) Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet 7: 81-102
17. Barski A, Zhao K (2009) Genomic location analysis by ChIP-Seq. J Cell Biochem 107: 11-18
18. Cuddapah S, Jothi R, Schones DE, Roh TY, Cui K, Zhao K (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
19. Jothi R, Cuddapah S, Barski A, Cui K, Zhao K (2008) Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 36: 5221-5231
20. Zheng M, Barrera LO, Ren B, Wu YN (2007) ChIP-chip: data, model, and analysis. Biometrics 63: 787-796
21. Bolton EC, So AY, Chaivorapol C, Haqq CM, Li H, Yamamoto KR (2007) Cell-and genespecific regulation of primary target genes by the androgen receptor. Genes Dev 21: 2005-2017
22. Kim TH, Abdullaev ZK, Smith AD, Ching KA, Loukinov DI, Green RD et al (2007) Analysis of the vertebrate insulator protein CTCFbinding sites in the human genome. Cell 128: 1231-1245
23. Zhang Y, Wu W, Cheng Y, King DC, Harris RS, Taylor J (2009) Primary sequence and epigenetic determinants of in vivo occupancy of genomic DNA by GATA1. Nucleic Acids Res 37: 7024-7038
24. Smeenk L, van Heeringen SJ, Koeppel M, van Driel MA, Bartels SJ, Akkers RC et al (2008) Characterization of genome-wide p53-binding sites upon stress response. Nucleic Acids Res 36: 3639-3654
25. Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc, Ser B 57: 289-300
26. Beverdam A, Koopman P (2006) Expression profiling of purified mouse gonadal somatic cells during the critical time window of sex determination reveals novel candidate genes for human sexual dysgenesis syndromes. Hum Mol Genet 15: 417-431
27. Jameson SA, Natarajan A, Cool J, DeFalco T, Maatouk DM, Mork L et al (2012) Temporal transcriptional profiling of somatic and germ cells reveals biased lineage priming of sexual fate in the fetal mouse gonad. PLoS Genet 8: e1002575
28. Nef S, Schaad O, Stallings NR, Cederroth CR, Pitetti JL, Schaer G et al (2005) Gene expression during sex determination reveals a robust female genetic program at the onset of ovarian development. Dev Biol 287(2): 361-377
29. Gautier L, Moller M, Friis-Hansen L, Knudsen S (2004) Alternative mapping of probes to genes for Affymetrix chips. BMC Bioinformatics 5: 111
30. Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP (2003) Summaries of Affymetrix Gene Chip probe level data. Nucleic Acids Res 31: e15
31. Smyth GK (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3
32. Wu JB, Chen K, Li Y, Lau YF, Shih JC (2009) Regulation of monoamine oxidase A by the SRY gene on the Y chromosome. FASEB J 23: 4029-4038