Pinpointing transcription factor binding sites from ChIP-seq data with SeqSite

BMC Systems Biology

Volumn 5, Issue SUPPL2, 2011, Pages

  Wang, Xi ^a,b   Zhang, Xuegong ^a  

^a TSINGHUA UNIVERSITY   (China)

^b UNIVERSITY OF NEWCASTLE   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

GA BINDING PROTEIN; RE1 SILENCING TRANSCRIPTION FACTOR; RE1-SILENCING TRANSCRIPTION FACTOR; REPRESSOR PROTEIN; STAT1 PROTEIN; STAT1 PROTEIN, HUMAN;

ARTICLE; BINDING SITE; BIOLOGY; CHROMATIN IMMUNOPRECIPITATION; CLUSTER ANALYSIS; DNA SEQUENCE; GENETIC DATABASE; GENETICS; GENOMICS; HUMAN; HUMAN GENOME; METABOLISM; METHODOLOGY;

BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GA-BINDING PROTEIN TRANSCRIPTION FACTOR; GENOME, HUMAN; GENOMICS; HUMANS; REPRESSOR PROTEINS; SEQUENCE ANALYSIS, DNA; STAT1 TRANSCRIPTION FACTOR;

EID: 84870369023     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-5-S2-S3     Document Type: Article

References (58)

1. Orlando V. Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 2000, 25:99-104. 10.1016/S0968-0004(99)01535-2, 10694875.
2. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, et al. Genome-wide location and function of DNA binding proteins. Science 2000, 290:2306-2309. 10.1126/science.290.5500.2306, 11125145.
3. Iyer VR, Horak CE, Scafe CS, Botstein D, Snyder M, Brown PO. Genomic binding sites of the yeast cell-cycle transcription factors SBF and MBF. Nature 2001, 409:533-538. 10.1038/35054095, 11206552.
4. Kim TH, Ren B. Genome-wide analysis of protein-DNA interactions. Annu Rev Genomics Hum Genet 2006, 7:81-102. 10.1146/annurev.genom.7.080505.115634, 16722805.
5. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 2007, 129:823-837. 10.1016/j.cell.2007.05.009, 17512414.
6. Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science 2007, 316:1497-1502. 10.1126/science.1141319, 17540862.
7. Mardis ER. ChIP-seq: welcome to the new frontier. Nat Methods 2007, 4:613-614. 10.1038/nmeth0807-613, 17664943.
8. Barski A, Zhao K. Genomic location analysis by ChIP-Seq. J Cell Biochem 2009, 107:11-18. 10.1002/jcb.22077, 19173299.
9. Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 2009, 10:669-680. 3191340, 19736561.
10. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26:1135-1145. 10.1038/nbt1486, 18846087.
11. Wold B, Myers RM. Sequence census methods for functional genomics. Nat Methods 2008, 5:19-21. 10.1038/nmeth1157, 18165803.
12. Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB, Wong E, Orlov YL, Zhang W, Jiang J, et al. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell 2008, 133:1106-1117. 10.1016/j.cell.2008.04.043, 18555785.
13. Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007, 448:553-560. 10.1038/nature06008, 2921165, 17603471.
14. Schmidt D, Stark R, Wilson MD, Brown GD, Odom DT. Genome-scale validation of deep-sequencing libraries. PLoS ONE 2008, 3:e3713. 10.1371/journal.pone.0003713, 2577887, 19002256.
15. Schmidt D, Wilson MD, Spyrou C, Brown GD, Hadfield J, Odom DT. ChIP-seq: Using high-throughput sequencing to discover protein-DNA interactions. Methods 2009, 48:240-248. 10.1016/j.ymeth.2009.03.001, 19275939.
16. Birney E, Stamatoyannopoulos JA, Dutta A, Guigo R, Gingeras TR, Margulies EH, Weng Z, Snyder M, Dermitzakis ET, Thurman RE, et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature 2007, 447:799-816. 10.1038/nature05874, 2212820, 17571346.
17. Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, et al. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res 2010, 38:D620-625. 10.1093/nar/gkp961, 2808953, 19920125.
18. Das MK, Dai HK. A survey of DNA motif finding algorithms. BMC Bioinformatics 2007, 8(Suppl 7):S21. 10.1186/1471-2105-8-S7-S21, 2099490, 18047721.
19. D'Haeseleer P. What are DNA sequence motifs?. Nat Biotechnol 2006, 24:423-425. 10.1038/nbt0406-423, 16601727.
20. Robertson G, Hirst M, Bainbridge M, Bilenky M, Zhao Y, Zeng T, Euskirchen G, Bernier B, Varhol R, Delaney A, et al. Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nat Methods 2007, 4:651-657. 10.1038/nmeth1068, 17558387.
21. 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, 27:66-75. 10.1038/nbt.1518, 2924752, 19122651.
22. 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, 24:1729-1730. 10.1093/bioinformatics/btn305, 2638869, 18599518.
23. Boyle AP, Guinney J, Crawford GE, Furey TS. F-Seq: a feature density estimator for high-throughput sequence tags. Bioinformatics 2008, 24:2537-2538. 10.1093/bioinformatics/btn480, 2732284, 18784119.
24. Tuteja G, White P, Schug J, Kaestner KH. Extracting transcription factor targets from ChIP-Seq data. Nucleic Acids Res 2009, 37:e113. 10.1093/nar/gkp536, 2761252, 19553195.
25. 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 Bioinformatics 2010, 11:369. 10.1186/1471-2105-11-369, 2912305, 20598134.
26. Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods 2009, 6:S22-32. 10.1038/nmeth.1371, 19844228.
27. 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, 26:1293-1300. 10.1038/nbt.1505, 2596672, 18978777.
28. 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, 5:829-834. 10.1038/nmeth.1246, 2917543, 19160518.
29. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nussbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol 2008, 9:R137. 10.1186/gb-2008-9-9-r137, 2592715, 18798982.
30. Nix DA, Courdy SJ, Boucher KM. Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks. BMC Bioinformatics 2008, 9:523. 10.1186/1471-2105-9-523, 2628906, 19061503.
31. 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, 36:5221-5231. 10.1093/nar/gkn488, 2532738, 18684996.
32. Kharchenko PV, Tolstorukov MY, Park PJ. Design and analysis of ChIP-seq experiments for DNA-binding proteins. Nat Biotechnol 2008, 26:1351-1359. 10.1038/nbt.1508, 2597701, 19029915.
33. 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.
34. Wilbanks EG, Facciotti MT. Evaluation of algorithm performance in ChIP-seq peak detection. PLoS ONE 2010, 5:e11471. 10.1371/journal.pone.0011471, 2900203, 20628599.
35. Lun DS, Sherrid A, Weiner B, Sherman DR, Galagan JE. A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data. Genome Biol 2009, 10:R142. 10.1186/gb-2009-10-12-r142, 2812949, 20028542.
36. Zhang X, Robertson G, Krzywinski M, Ning K, Droit A, Jones S, Gottardo R. PICS: Probabilistic Inference for ChIP-seq. Biometrics 2011, 67:151-163. 10.1111/j.1541-0420.2010.01441.x, 20528864.
37. Guo Y, Papachristoudis G, Altshuler RC, Gerber GK, Jaakkola TS, Gifford DK, Mahony S. Discovering homotypic binding events at high spatial resolution. Bioinformatics 2010, 26:3028-3034. 10.1093/bioinformatics/btq590, 2995123, 20966006.
38. SeqSite website. , http://bioinfo.au.tsinghua.edu.cn/seqsite
39. Bottinger EP, Shelley CS, Farokhzad OC, Arnaout MA. The human beta 2 integrin CD18 promoter consists of two inverted Ets cis elements. Mol Cell Biol 1994, 14:2604-2615. 10.1128/MCB.14.4.2604, 358628, 7511209.
40. Rosmarin AG, Caprio DG, Kirsch DG, Handa H, Simkevich CP. GABP and PU.1 compete for binding, yet cooperate to increase CD18 (beta 2 leukocyte integrin) transcription. J Biol Chem 1995, 270:23627-23633. 10.1074/jbc.270.40.23627, 7559529.
41. Rosmarin AG, Resendes KK, Yang Z, McMillan JN, Fleming SL. GA-binding protein transcription factor: a review of GABP as an integrator of intracellular signaling and protein-protein interactions. Blood Cells Mol Dis 2004, 32:143-154. 10.1016/j.bcmd.2003.09.005, 14757430.
42. Matys V, Fricke E, Geffers R, Gossling E, Haubrock M, Hehl R, Hornischer K, Karas D, Kel AE, Kel-Margoulis OV, et al. TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 2003, 31:374-378. 10.1093/nar/gkg108, 165555, 12520026.
43. Bailey TL, Gribskov M. Combining evidence using p-values: application to sequence homology searches. Bioinformatics 1998, 14:48-54. 10.1093/bioinformatics/14.1.48, 9520501.
44. Bruce AW, Donaldson IJ, Wood IC, Yerbury SA, Sadowski MI, Chapman M, Gottgens B, Buckley NJ. Genome-wide analysis of repressor element 1 silencing transcription factor/neuron-restrictive silencing factor (REST/NRSF) target genes. Proc Natl Acad Sci U S A 2004, 101:10458-10463. 10.1073/pnas.0401827101, 478591, 15240883.
45. Nickel J, Short ML, Schmitz A, Eggert M, Renkawitz R. Methylation of the mouse M-lysozyme downstream enhancer inhibits heterotetrameric GABP binding. Nucleic Acids Res 1995, 23:4785-4792. 10.1093/nar/23.23.4785, 307465, 8532519.
46. Wormald S, Hilton DJ, Smyth GK, Speed TP. Proximal genomic localization of STAT1 binding and regulated transcriptional activity. BMC Genomics 2006, 7:254. 10.1186/1471-2164-7-254, 1618399, 17032459.
47. Rabinovich A, Jin VX, Rabinovich R, Xu X, Farnham PJ. E2F in vivo binding specificity: comparison of consensus versus nonconsensus binding sites. Genome Res 2008, 18:1763-1777. 10.1101/gr.080622.108, 2577861, 18836037.
48. Farnham PJ. Insights from genomic profiling of transcription factors. Nat Rev Genet 2009, 10:605-616. 10.1038/nrg2636, 2846386, 19668247.
49. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, et al. Diversity and complexity in DNA recognition by transcription factors. Science 2009, 324:1720-1723. 10.1126/science.1162327, 2905877, 19443739.
50. Jiang C, Pugh BF. Nucleosome positioning and gene regulation: advances through genomics. Nat Rev Genet 2009, 10:161-172.
51. Fan X, Lamarre-Vincent N, Wang Q, Struhl K. Extensive chromatin fragmentation improves enrichment of protein binding sites in chromatin immunoprecipitation experiments. Nucleic Acids Res 2008, 36:e125. 10.1093/nar/gkn535, 2577354, 18765474.
52. Wang J, Huda A, Lunyak VV, Jordan IK. A Gibbs sampling strategy applied to the mapping of ambiguous short-sequence tags. Bioinformatics 2010, 26:2501-2508. 10.1093/bioinformatics/btq460, 2951085, 20871106.
53. QuEST website. , http://mendel.stanford.edu/sidowlab/downloads/quest
54. PeakSeq website. , http://archive.gersteinlab.org/proj/PeakSeq
55. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36:e105. 10.1093/nar/gkn425, 2532726, 18660515.
56. Benjamini Y, Hochberg Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J R Stat Soc Ser B 1995, 57:289-300.
57. Qi Y, Rolfe A, MacIsaac KD, Gerber GK, Pokholok D, Zeitlinger J, Danford T, Dowell RD, Fraenkel E, Jaakkola TS, et al. High-resolution computational models of genome binding events. Nat Biotechnol 2006, 24:963-970. 10.1038/nbt1233, 16900145.
58. Reiss DJ, Facciotti MT, Baliga NS. Model-based deconvolution of genome-wide DNA binding. Bioinformatics 2008, 24:396-403. 10.1093/bioinformatics/btm592, 18056063.