Computing exact P-values for DNA motifs

Bioinformatics

Volumn 23, Issue 5, 2007, Pages 531-537

  Zhang, Jing ^a   Jiang, Bo ^a   Li, Ming ^a,b   Tromp, John ^c   Zhang, Xuegong ^a   Zhang, Michael Q ^a,d  

^a TSINGHUA UNIVERSITY   (China)

^b UNIVERSITY OF WATERLOO   (Canada)

^c CWI   (Netherlands)

^d Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ACCURACY; AREA UNDER THE CURVE; ARTICLE; BINDING SITE; CALCULATION; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENETIC ALGORITHM; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROBABILITY; PROMOTER REGION; RECEIVER OPERATING CHARACTERISTIC; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; STATISTICAL SIGNIFICANCE; TIME;

EID: 34047159557     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl662     Document Type: Article

References (29)

1. Bailey,T.L. and Gribskov,M. (1998) Combining evidence using P-values: application to sequence homology searches. Bioinformatics, 14, 48-54.
2. Bailey,T.L. and 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. pp. 28-36.
3. Beckstette,M. et al. (2006) Fast index based algorithms and software for matching position specific scoring matrices. BMC Bioinformatics, 7, 389.
4. Bejerano,G. et al. (2004) Efficient exact P-value computation for small sample, sparse, and surprising categorical data. J. Comp. Biol., 11, 867-886.
5. Brendel,V. et al. (1986) Linguistics of nucleotide sequences: Morphology and comparison of vocabularies. J. Biomol. Struct. Dyn., 4.
6. Chryssaphinou,O. and Papastavridis,S. (1988) A limit theorem for the number of non-overlapping occurrences of a pattern in a sequence of independent trials. J. Appl. Prob., 25, 428-431.
7. Denise,A. et al. (2001) Assessing statistical significance of overrepresented oligonucleotides. In WABI'01. pp. 85-97.
8. Frith,M.C. et al. (2004) Detection of functional DNA motifs via statistical over-representation. Nucleic Acids Res., 32, 1372-1381.
9. Gentleman,J. and Mullin,R. (1989) The distribution of the frequency of occurence of nucleotide subsequence, based on their overlap capability. Biometrics, 45, 35-52.
10. Godbole,A.P. (1991) Poisson approximations for runs and patterns of rare events. Adv. Appl. Prob., 23, 851-865.
11. Goulden,I.P. and Jackson,D.M. (1983) Combinatorial Enumeration. Wiley.
12. Guibas,L.J. and Odlyzko,A.M. (1981) Strings overlaps, pattern matching and nontransitive games. J. Combinat. Theory, Series A 30.
13. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignment of multiple sequences. Bioinformatics, 15.
14. Hertzberg,L. et al. (2005) Finding motifs in promoter regions. J. Comp. Biol., 12, 314-330.
15. Keich,U. et al. (2004) On spaced seeds for similarity search. Discrete Appli. Math, 138, 253-263.
16. Kleffe,J. and Langbecker,U. (1990) Exact computation of pattern probabilities in random sequences generated by Markov chains. Comp. Appl. Biosci., 6, 347-353.
17. Leung,M.Y. et al. (1996) Over and underrepresentation of short DNA words in Herpes virus genomes. J. Comp. Biol., 3, 345-360.
18. Li,M. Superiority and complexity of the spaced seeds. In SODA'06.
19. Ma,B. et al. (2002) PatternHunter: Faster and more sensitive homology search. Bioinformatics, 18, 440-445.
20. Nagarajan,N. et al. (2005) Computing the P-value of the information content from an alignment of multiple sequences. Bioinformatics, 21 (Suppl. 1), ISMB '05, pp. i311-i318.
21. Rajewsky,N. et al. (2002) Computational detection of genomic cis regulatory modules, applied to body patterning in the early Drosophila embryo. BMC Bioinformatics, 3, 30.
22. Régnier,M. (2001) A unified approach to word occurrence probabilities. Discrete Appl Math., 104, 259-280.
23. Staden,R. (1998) Methods for calculating the probabilities of finding patterns in sequences. Comput. Appl. Biosci., 5, 89-96.
24. Schbath,S. (1995) Compound Poisson approximation of word counts in DNA sequences. ESAIM: Probab. Stati., 1, 1-16.
25. Stormo,G.D. (2000) DNA binding sites: Representation and discovery. Bioinformatics, 16, 16-23.
26. Tronche,F. et al. (1997) Analysis of the distribution of binding sites for a tissue-specific transcription factor in the vertebrate genome. J. Mol. Biol., 266, 234-245.
27. Thijs,G. et al. (2001) A Gibbs sampling method to detect over-represented motifs in upstream regions of coexpressed genes. In Proceedings Recomb'2001. pp. 305-312.
28. Waterman,M.S. (1995) Introduction to Computational Biology. Chapman & Hall.
29. Zhu,J. and Zhang,M.Q. (1999) SCPD: A promoter database of yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.