A deterministic motif finding algorithm with application to the human genome

Bioinformatics

Volumn 22, Issue 9, 2006, Pages 1047-1054

  Hon, Lawrence S ^a   Jain, Ajay N ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ENDOTHELIN 1; ENOLASE; HEAT SHOCK PROTEIN; PHOSPHOGLYCERATE MUTASE; TRANSCRIPTION FACTOR; TRANSFERRIN RECEPTOR; VASCULOTROPIN;

ALGORITHM; ARTICLE; BINDING SITE; BIOINFORMATICS; COMPUTER PROGRAM; CONTROLLED STUDY; DNA SEQUENCE; GENE FREQUENCY; GENOME ANALYSIS; HUMAN; HUMAN GENOME; NONHUMAN; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROTEIN BINDING; PROTEIN MOTIF; SCORING SYSTEM; SEQUENCE ANALYSIS;

EID: 33646158909     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl037     Document Type: Article

References (39)

1. Altschul,S.F. (1989) Gap costs for multiple sequence alignment. J. Theor. Biol., 138, 297-309.
2. Altschul,S.F. et al. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
3. Bailey,T.L. and Elkan,C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proc. Int. Conf. Intell. Syst. Mol. Biol., 2, 28-36.
4. Ball,C.A. et al. (2005) The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res., 33, D580-D582.
5. Bernardi,G. (1995) The human genome: Organization and evolutionary history. Annu. Rev. Genet., 29, 445-476.
6. Buhler,J. and Tompa,M. (2002) Finding motifs using random projections. J. Comput. Biol., 9, 225-242.
7. Bussemaker,H.J. et al. (2000) Building a dictionary for genomes: identification of presumptive regulatory sites by statistical analysis. Proc. Natl Acad. Sci. USA, 97, 10096-10100.
8. Bussemaker,H.J. et al. (2001) Regulatory element detection using correlation with expression. Nat. Genet., 27, 167-171.
9. Conlon,E.M. et al. (2003) Integrating regulatory motif discovery and genome-wide expression analysis. Proc. Natl Acad. Sci. USA, 100, 3339-3344.
10. Fernandez,P.C. et al. (2003) Genomic targets of the human c-Myc protein. Genes Dev., 17, 1115-1129.
11. Guhathakurta,D. and Stormo,G.D. (2001) Identifying target sites for cooperatively binding factors. Bioinformatics, 17, 608-621.
12. Gupta,M. and Liu,J.S. (2005) De novo cis-regulatory module elicitation for eukaryotic genomes. Proc. Natl Acad. Sci. USA, 102, 7079-7084.
13. Gupta,S.K. et al. (1995) Improving the practical space and time efficiency of the shortest-paths approach to sum-of-pairs multiple sequence alignment. J. Comput. Biol., 2, 459-472.
14. Hertz,G.Z. and Stormo,G.D. (1999) Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics, 15, 563-577.
15. Hon,L.S. and Jain,A.N. (2003) Compositional structure of repetitive elements is quantitatively related to co-expression of gene pairs. J Mol Biol, 332, 305-310.
16. Keles,S. et al. (2002) Identification of regulatory elements using a feature selection method. Bioinformatics, 18, 1167-1175.
17. Levine,M. and Tjian,R. (2003) Transcription regulation and animal diversity. Nature, 424, 147-151.
18. Li,H. et al. (2002) Identification of the binding sites of regulatory proteins in bacterial genomes. Proc. Natl Acad. Sci. USA, 99, 11772-11777.
19. Liu,X. et al. (2001) BioProspector: Discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes. Pac. Symp. Biocomput., 127-138.
20. Liu,X.S. et al. (2002) An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments. Nat. Biotechnol., 20, 835-839.
21. Liu,Y. et al. (2004) Eukaryotic regulatory element conservation analysis and identification using comparative genomics. Genome Res., 14, 451-458.
22. Mccue,L. et al. (2001) Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes. Nucleic Acids Res., 29, 774-782.
23. Nobrega,M.A. et al. (2003) Scanning human gene deserts for long-range enhancers. Science, 302, 413.
24. Ota,T. et al. (2004) Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat. Genet., 36, 40-45.
25. Pavesi,G. et al. (2001) An algorithm for finding signals of unknown length in DNA sequences. Bioinformatics, 17 (Suppl. 1), S207-S214.
26. Pesole,G. et al. (1999) Isochore specificity of AUG initiator context of human genes. FEBS Lett., 464, 60-62.
27. Roth,F.P. et al. (1998) Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation. Nat. Biotechnol., 16, 939-945.
28. Sinha,S. and Tompa,M. (2003) YMF: A program for discovery of novel transcription factor binding sites by statistical overrepresentation. Nucleic Acids Res., 31, 3586-3588.
29. Smit,A.F.A., Hubley,R. and Green,P. (1996-2004) RepeatMasker Open-3.0.
30. Stuart,J.M. et al. (2003) A gene-coexpression network for global discovery of conserved genetic modules. Science, 302, 249-255.
31. Thijs,G. et al. (2001) A higher-order background model improves the detection of promoter regulatory elements by Gibbs sampling. Bioinformatics, 17, 1113-1122.
32. Tompa,M. et al. (2005) Assessing computational tools for the discovery of transcription factor binding sites. Nat. Biotechnol., 23, 137-144.
33. van Helden,J. (2003) Regulatory sequence analysis tools. Nucleic Acids Res., 31, 3593-3596.
34. Wang,T. and Stormo,G.D. (2003) Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics, 19, 2369-2380.
35. Wingender,E. et al. (2001) The TRANSFAC system on gene expression regulation. Nucleic Acids Res., 29, 281-283.
36. Workman,C.T. and Stormso,G.D. (2000) ANN-Spec: A method for discovering transcription factor binding sites with improved specificity. Pac. Symp. Biocomput., 467-478.
37. Zeller,K.I. et al. (2003) An integrated database of genes responsive to the Myc oncogenic transcription factor: Identification of direct genomic targets. Genome Biol., 4, R69.
38. Zhou,Q. and Wong,W.H. (2004) CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. Proc. Natl Acad. Sci. USA, 101, 12114-12119.
39. Zhu,Z. et al. (2002) Computational identification of transcription factor binding sites via a transcription-factor-centric clustering (TFCC) algorithm. J. Mol. Biol., 318, 71-81.