The Next Generation of Transcription Factor Binding Site Prediction

PLoS Computational Biology

Volumn 9, Issue 9, 2013, Pages

  Mathelier, Anthony ^a   Wasserman, Wyeth W ^a  

^a UNIVERSITY OF BRITISH COLUMBIA   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; BINDING SITES; DNA; DNA SEQUENCES; FORECASTING; HIDDEN MARKOV MODELS; MATRIX ALGEBRA; NUCLEOTIDES; PULSE WIDTH MODULATION; TRANSCRIPTION;

BINDING SITE PREDICTIONS; BINDING-SITES; COMPUTATIONAL PREDICTIONS; DNA-PROTEIN INTERACTION; FLEXIBLE MODEL; GENE-REGULATION; POSITION WEIGHTS; TRANSCRIPTION FACTOR BINDING SITES; TRANSCRIPTIONAL LEVELS; WEIGHT MATRICES;

TRANSCRIPTION FACTORS;

STAT4 PROTEIN; STAT6 PROTEIN; TRANSCRIPTION FACTOR;

ACCURACY; AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; CHROMATIN IMMUNOPRECIPITATION; HIDDEN MARKOV MODEL; MOLECULAR SIZE; POSITION WEIGHT MATRIX; PREDICTION; PROTEIN ANALYSIS; PROTEIN DNA INTERACTION;

BINDING SITES; CHROMATIN IMMUNOPRECIPITATION; DNA; PROBABILITY; TRANSCRIPTION FACTORS;

EID: 84884695174     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1003214     Document Type: Article

References (68)

1. Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, et al. (2009) Diversity and complexity in DNA recognition by transcription factors. Science (New York, NY) 324: 1720-3.
2. Wasserman WW, Sandelin A, (2004) Applied bioinformatics for the identification of regulatory elements. Nature reviews Genetics 5: 276-87.
3. Stark A, Lin MF, Kheradpour P, Pedersen JS, Parts L, et al. (2007) Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature 450: 219-32.
4. Bernard V, Lecharny A, Brunaud V, (2010) Improved detection of motifs with preferential location in promoters. Genome 53: 739-52.
5. Arvey A, Agius P, Noble WS, Leslie C, (2012) Sequence and chromatin determinants of cell-type-specific transcription factor binding. Genome research 22: 1723-34.
6. Ho Sui SJ, Mortimer JR, Arenillas DJ, Brumm J, Walsh CJ, et al. (2005) oPOSSUM: identification of over-represented transcription factor binding sites in co-expressed genes. Nucleic acids research 33: 3154-64.
7. Ho Sui SJ, Fulton DL, Arenillas DJ, Kwon AT, Wasserman WW, (2007) oPOSSUM: integrated tools for analysis of regulatory motif over-representation. Nucleic acids research 35: W245-52.
8. Stormo GD, (2013) Modeling the specificity of protein-dna interactions. Quantitative Biology 1: 115-130.
9. Luscombe NM, Laskowski RA, Thornton JM, (2001) Amino acid-base interactions: a three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic acids research 29: 2860-74.
10. Man TK, Stormo GD, (2001) Non-independence of Mnt repressor-operator interaction determined by a new quantitative multiple fluorescence relative affinity (QuMFRA) assay. Nucleic acids research 29: 2471-8.
11. Bulyk ML, Johnson PLF, Church GM, (2002) Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic acids research 30: 1255-1261.
12. Berger MF, Philippakis AA, Qureshi AM, He FS, Estep PW, et al. (2006) Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities. Nature biotechnology 24: 1429-35.
13. Barash Y, Elidan G, Friedman N, Kaplan T (2003) Modeling dependencies in protein-DNA binding sites. In: Proceedings of the seventh annual international conference on Computational molecular biology- RECOMB '03. New York, New York, USA: ACM Press, pp. 28-37.
14. Tomovic A, Oakeley EJ, (2007) Position dependencies in transcription factor binding sites. Bioinformatics (Oxford, England) 23: 933-41.
15. Zhou Q, Liu JS, (2004) Modeling within-motif dependence for transcription factor binding site predictions. Bioinformatics (Oxford, England) 20: 909-16.
16. Mukherjee S, Berger MF, Jona G, Wang XS, Muzzey D, et al. (2004) Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays. Nature genetics 36: 1331-9.
17. Weirauch MT, Cote A, Norel R, Annala M, Zhao Y, et al. (2013) Evaluation of methods for modeling transcription factor sequence specificity. Nature biotechnology 31: 126-34.
18. Zhao Y, Ruan S, Pandey M, Stormo GD, (2012) Improved models for transcription factor binding site identification using nonindependent interactions. Genetics 191: 781-90.
19. Siddharthan R, (2010) Dinucleotide weight matrices for predicting transcription factor binding sites: generalizing the position weight matrix. PloS one 5: e9722.
20. Sandelin A, Wasserman WW, (2005) Prediction of nuclear hormone receptor response elements. Molecular endocrinology (Baltimore, Md) 19: 595-606.
21. Lyakhov IG, Krishnamachari A, Schneider TD, (2008) Discovery of novel tumor suppressor p53 response elements using information theory. Nucleic acids research 36: 3828-33.
22. Riley T, Yu X, Sontag E, Levine A, (2009) The p53HMM algorithm: using profile hidden markov models to detect p53-responsive genes. BMC Bioinformatics 10: 111.
23. Harr R, Häggström M, Gustafsson P, (1983) Seach algorithm for pattern match analysis of nucleic acid sequences. Nucleic Acids Research 11: 2943-2957.
24. Staden R, (1984) Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Research 12: 505-519.
25. Ehret GB, Reichenbach P, Schindler U, Horvath CM, Fritz S, et al. (2001) DNA binding specificity of different STAT proteins. Comparison of in vitro specificity with natural target sites. The Journal of biological chemistry 276: 6675-88.
26. Soldaini E, John S, Moro S, Bollenbacher J, Schindler U, et al. (2000) DNA Binding Site Selection of Dimeric and Tetrameric Stat5 Proteins Reveals a Large Repertoire of Divergent Tetrameric Stat5a Binding Sites. Molecular and Cellular Biology 20: 389-401.
27. Reid JE, Evans KJ, Dyer N, Wernisch L, Ott S, (2010) Variable structure motifs for transcription factor binding sites. BMC genomics 11: 30.
28. Lin Th, Ray P, Sandve GK, Uguroglu S, Xing EP (2008) BayCis: A Bayesian Hierarchical HMM for Cis-Regulatory Module Decoding in Metazoan Genomes. In: Vingron M, Wong L, editors, RECOMB'08 Proceedings of the 12th annual international conference on Research in computational molecular biology. Springer Berlin Heidelberg, pp. 66-81.
29. Wasson T, Hartemink AJ, (2009) An ensemble model of competitive multi-factor binding of the genome. Genome research 19: 2101-12.
30. Levkovitz L, Yosef N, Gershengorn MC, Ruppin E, Sharan R, et al. (2010) A Novel HMM-Based Method for Detecting Enriched Transcription Factor Binding Sites Reveals RUNX3 as a Potential Target in Pancreatic Cancer Biology. PloS one 5: e14423.
31. Salama RA, Stekel DJ, (2010) Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction. Nucleic acids research 38: e135.
32. Mehta P, Schwab DJ, Sengupta AM, (2011) Statistical Mechanics of Transcription-Factor Binding Site Discovery Using Hidden Markov Models. Journal of statistical physics 142: 1187-1205.
33. Marinescu VD, Kohane IS, Riva A, (2005) MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes. BMC bioinformatics 6: 79.
34. Marinescu VD, Kohane IS, Riva A, (2005) The MAPPER database: a multi-genome catalog of putative transcription factor binding sites. Nucleic acids research 33: D91-7.
35. Raman R, Overton GC (1994) Application of hidden Markov modeling to the characterization of transcription factor binding sites. In: Proceedings of the Twenty-Seventh Hawaii International Conference on System Sciences HICSS-94. IEEE Comput. Soc. Press, pp. 275-283.
36. Durbin R, Edddy S, Krogh A, Mitchison G (1998) Biological sequence analysis Probabilistic models of proteins and nucleic acids. Cambridge: Cambridge University Press.
37. Ben-Gal I, Shani A, Gohr A, Grau J, Arviv S, et al. (2005) Identification of transcription factor binding sites with variable-order Bayesian networks. Bioinformatics (Oxford, England) 21: 2657-66.
38. Johnson DS, Mortazavi A, Myers RM, Wold B, (2007) Genome-wide mapping of in vivo protein- DNA interactions. Science (New York, NY) 316: 1497-502.
39. ENCODE (2004) The ENCODE (ENCyclopedia Of DNA Elements) Project. Science (New York, NY) 306: 636-40.
40. Segal E, Fondufe-Mittendorf Y, Chen L, Thå ström A, Field Y, et al. (2006) A genomic code for nucleosome positioning. Nature 442: 772-8.
41. Schneider TD, Stephens RM, (1990) Sequence logos: a new way to display consensus sequences. Nucleic acids research 18: 6097-6100.
42. Schuster-Böckler B, Schultz J, Rahmann S, (2004) HMM Logos for visualization of protein families. BMC bioinformatics 5: 7.
43. Bailey TL, Elkan C (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. In: Proceedings of the second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, pp. 28-36.
44. Bailey TL, Gribskov M, (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics (Oxford, England) 14: 48-54.
45. Wilbanks EG, Facciotti MT, (2010) Evaluation of algorithm performance in ChIP-seq peak detection. PloS one 5: e11471.
46. Wilcoxon F, (1945) Individual Comparisons by Ranking Methods. Biometrics Bulletin 1: 80-83.
47. Benjamini Y, Hochberg Y, (1995) Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B (Methodological) 57: 289-300.
48. Benos PV, Lapedes AS, Stormo GD, (2002) Probabilistic Code for DNA Recognition by Proteins of the EGR Family. Journal of Molecular Biology 323: 701-727.
49. Benos PV, Lapedes AS, Fields D, Stormo GD, (2001) SAMIE: Statistical algorithm for modeling interaction energies. In: Pacific Symposium on Biocomputing volume 1266: 115-126.
50. Benos PV, Bulyk ML, Stormo GD, (2002) Additivity in protein-DNA interactions: how good an approximation is it? Nucleic acids research 30: 4442-51.
51. Spearman C (1904) The proof and measurement of association between two things. American Journal of Psychology: 72-101.
52. Maerkl SJ, Quake SR, (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science (New York, NY) 315: 233-7.
53. Frith MC, Saunders NFW, Kobe B, Bailey TL, (2008) Discovering sequence motifs with arbitrary insertions and deletions. PLoS computational biology 4: e1000071.
54. Wei L, Vahedi G, Sun HW, Watford WT, Takatori H, et al. (2010) Discrete roles of STAT4 and STAT6 transcription factors in tuning epigenetic modifications and transcription during T helper cell differentiation. Immunity 32: 840-51.
55. Granek Ja, Clarke ND, (2005) Explicit equilibrium modeling of transcription-factor binding and gene regulation. Genome biology 6: R87.
56. Roider HG, Kanhere A, Manke T, Vingron M, (2007) Predicting transcription factor affinities to DNA from a biophysical model. Bioinformatics (Oxford, England) 23: 134-41.
57. Drawid A, Gupta N, Nagaraj VH, Gélinas C, Sengupta AM, (2009) OHMM: a Hidden Markov Model accurately predicting the occupancy of a transcription factor with a self-overlapping binding motif. BMC bioinformatics 10: 208.
58. Siggers T, Duyzend MH, Reddy J, Khan S, Bulyk ML, (2011) Non-DNA-binding cofactors enhance DNA-binding specificity of a transcriptional regulatory complex. Molecular Systems Biology 7: 1-14.
59. Borneman AR, Gianoulis Ta, Zhang ZD, Yu H, Rozowsky J, et al. (2007) Divergence of transcription factor binding sites across related yeast species. Science (New York, NY) 317: 815-9.
60. Kasowski M, Grubert F, Heffelfinger C, Hariharan M, Asabere A, et al. (2010) Variation in transcription factor binding among humans. Science (New York, NY) 328: 232-5.
61. Felice B, Cattoglio C, Cittaro D, Testa A, Miccio A, et al. (2009) Transcription factor binding sites are genetic determinants of retroviral integration in the human genome. PloS one 4: e4571.
62. Portales-Casamar E, Kirov S, Lim J, Lithwick S, Swanson MI, et al. (2007) PAZAR: a framework for collection and dissemination of cis-regulatory sequence annotation. Genome biology 8: R207.
63. Portales-Casamar E, Arenillas D, Lim J, Swanson MI, Jiang S, et al. (2009) The PAZAR database of gene regulatory information coupled to the ORCA toolkit for the study of regulatory sequences. Nucleic acids research 37: D54-60.
64. Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, et al. (2010) JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 38 (Database issue): D105-10.
65. Bailey TL, Boden M, Buske FA, Frith M, Grant CE, et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic acids research 37: W202-8.
66. R Development Core Team (2011) R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/. ISBN 3-900051-07-0.
67. Cock P, Antao T, Chang J, Chapman B, Cox C, et al. (2009) Biopython: freely available python tools for computational molecular biology and bioinformatics. Bioinformatics 25: 1422-1423.
68. Schliep A, Georgi B, Rungsarityotin W (2004) The General Hidden Markov Model Library: Analyzing Systems with Unobservable States. In: Proceedings of the Heinz-Billing-Price. p. 15.