NEXT-peak: A normal-exponential two-peak model for peak-calling in ChIP-seq data

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Kim, Nak Kyeong ^a   Jayatillake, Rasika V ^a   Spouge, John L ^b  

^a OLD DOMINION UNIVERSITY   (United States)

^b NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

ChIP seq; Continuous mixture; Goodness of fit; Normal exponential distribution; Poisson regression

Indexed keywords

STAT1 PROTEIN; TRANSCRIPTION FACTOR;

ACCURACY; ALGORITHM; ARTICLE; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; GENE MAPPING; GENE SEQUENCE; HIGH THROUGHPUT SEQUENCING; NORMAL EXPONENTIAL TWO PEAK MODEL; PROTEIN MOTIF; STATISTICAL MODEL;

CHROMATIN IMMUNOPRECIPITATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MODELS, STATISTICAL; NUCLEOTIDE MOTIFS; SOFTWARE;

EID: 84878008923     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-349     Document Type: Article

References (20)

1. Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316(5830):1497-1502. 10.1126/science.1141319, 17540862.
2. Wilbanks EG, Facciotti MT. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS One 2010, 5(7):e11471. 10.1371/journal.pone.0011471, 2900203, 20628599.
3. Laajala TD, Raghav S, Tuomela S, Lahesmaa R, Aittokallio T, Elo LL. A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments. BMC Genomics 2009, 10:618. 10.1186/1471-2164-10-618, 2804666, 20017957.
4. Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6(11 Suppl):S22-S32.
5. Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nat Biotechnol 2009, 27(1):66-75. 10.1038/nbt.1518, 2924752, 19122651.
6. Fejes AP, Robertson G, Bilenky M, Varhol R, Bainbridge M, Jones SJ. FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology. Bioinformatics 2008, 24(15):1729-1730. 10.1093/bioinformatics/btn305, 2638869, 18599518.
7. Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008, 5(7):621-628. 10.1038/nmeth.1226, 18516045.
8. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9(9):R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
9. Ji H, Jiang H, Ma W, Johnson DS, Myers RM, Wong WH. An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol 2008, 26(11):1293-1300. 10.1038/nbt.1505, 2596672, 18978777.
10. Qin ZS, Yu J, Shen J, Maher CA, Hu M, Kalyana-Sundaram S, Chinnaiyan AM. HPeak: an HMM-based algorithm for defining read-enriched regions in ChIP-Seq data. BMC Bioinforma 2010, 11:369.
11. Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 2008, 26(12):1351-1359. 10.1038/nbt.1508, 2597701, 19029915.
12. Jothi R, Cuddapah S, Barski A, Cui K, Zhao K. Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data. Nucleic Acids Res 2008, 36(16):5221-5231. 10.1093/nar/gkn488, 2532738, 18684996.
13. Valouev A, Johnson DS, Sundquist A, Medina C, Anton E, Batzoglou S, Myers RM, Sidow A. Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. Nat Methods 2008, 5(9):829-834. 10.1038/nmeth.1246, 2917543, 19160518.
14. Kuznetsov VA, Singh O, Jenjaroenpun P. Statistics of protein-DNA binding and the total number of binding sites for a transcription factor in the mammalian genome. BMC Genomics 2010, 11(Suppl 1):S12. 10.1186/1471-2164-11-S1-S12, 3005917, 21143795.
15. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 2007, 4(8):651-657. 10.1038/nmeth1068, 17558387.
16. Sandelin A, Alkema W, Engstrom P, Wasserman WW, Lenhard B. JASPAR: an open-access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res 2004, 32(Database issue):D91-D94. 308747, 14681366.
17. Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 2009, 10(3):R25. 10.1186/gb-2009-10-3-r25, 2690996, 19261174.
18. Staden R. Methods for calculating the probabilities of finding patterns in sequences. Comput Appl Biosci 1989, 5(2):89-96.
19. Altschul SF, Koonin EV. Iterated profile searches with PSI-BLAST-a tool for discovery in protein databases. Trends Biochem Sci 1998, 23(11):444-447. 10.1016/S0968-0004(98)01298-5, 9852764.
20. Tharakaraman K, Marino-Ramirez L, Sheetlin S, Landsman D, Spouge JL. Alignments anchored on genomic landmarks can aid in the identification of regulatory elements. Bioinformatics 2005, 21:I440-I448. 10.1093/bioinformatics/bti1028, 1317086, 15961489.