Compo: Composite motif discovery using discrete models

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Sandve, Geir Kjetil ^a,c   Abul, Osman ^b   Drabløs, Finn ^a  

^a NORWEGIAN UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Norway)

^b TOBB UNIVERSITY OF ECONOMICS AND TECHNOLOGY   (Turkey)

^c UNIVERSITY OF OSLO   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

BIOMOLECULAR SEQUENCES; DISCRETE MODELING; MULTI-OBJECTIVE EVALUATIONS; MULTIPLE PARAMETERS; PARAMETER SETTING; SIGNIFICANCE MEASURES; SPATIAL CLUSTERING; THRESHOLD SETTING;

PULSE WIDTH MODULATION;

DNA SEQUENCES;

ALGORITHM; ARTICLE; BINDING SITE; BIOLOGICAL MODEL; BIOLOGY; COMPUTER PROGRAM; GENETICS; METHODOLOGY; NUCLEOTIDE SEQUENCE; PROTEIN MOTIF;

ALGORITHMS; AMINO ACID MOTIFS; BASE SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; MODELS, GENETIC; SOFTWARE;

EID: 58149494592     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-527     Document Type: Article

References (34)

1. Bailey TL Elkan CE Unsupervised learning of multiple motifs in biopolymers using expectation maximization Machine Learning 1995, 21:51-80
2. Hughes JD Estep PW Tavazoie S Church GM Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae J Mol Biol 2000, 296(5):1205-14 10698627
3. Tompa M Li N Bailey TL Church GM De Moor B Eskin E Favorov AV Frith MC Fu Y Kent WJ Makeev VJ Mironov AA Noble WS Pavesi G Pesole G Regnier M Simonis N Sinha S Thijs G van Helden J Vandenbogaert M Weng Z Workman C Ye C Zhu Z Assessing computational tools for the discovery of transcription factor binding sites Nat Biotechnol 2005, 23:137-44 15637633
4. Kato M Hata N Banerjee N Futcher B Zhang MQ Identifying combinatorial regulation of transcription factors and binding motifs Genome Biol 2004, 5(8):R56 507881 15287978
5. Wray GA Hahn MW Abouheif E Balhoff JP Pizer M Rockman MV Romano LA The evolution of transcriptional regulation in eukaryotes Mol Biol Evol 2003, 20(9):1377-419 12777501
6. Marsan L Sagot MF Algorithms for extracting structured motifs using a suffix tree with an application to promoter and regulatory site consensus identification J Comput Biol 2000, 7(3-4):345-62 11108467
7. Aerts S Van Loo P Thijs G Moreau Y De Moor B Computational detection of cis-regulatory modules Bioinformatics 2003, 19(Suppl 2):II5-II14 14534164
8. Sandve GK Drabløs F A survey of motif discovery methods in an integrated framework Biol Direct 2006, 1(11) 1479319 16600018
9. Zhou Q Wong WH CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling Proc Natl Acad Sci USA 2004, 101(33):12114-9 514443 15297614
10. Xing EP Wu W Jordan MI Karp RM Logos: A modular bayesian model for de novo motif detection J Bioinform Comput Biol 2004, 2:127-54 15272436
11. Gupta M Liu JS De novo cis-regulatory module elicitation for eukaryotic genomes Proc Natl Acad Sci USA 2005, 102(20):7079-84 1129096 15883375
12. Frith MC Hansen U Weng Z Detection of cis-element clusters in higher eukaryotic DNA Bioinformatics 2001, 17(10):878-89 11673232
13. Johansson O Alkema W Wasserman WW Lagergren J Identification of functional clusters of transcription factor binding motifs in genome sequences: The MSCAN algorithm Bioinformatics 2003, 19(Suppl 1):i169-76 12855453
14. Wagner A Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes Bioinformatics 1999, 15(10):776-84 10705431
15. Sharan R Ovcharenko I Ben-Hur A Karp RM CREME: A framework for identifying cis-regulatory modules in human-mouse conserved segments Bioinformatics 2003, 19(Suppl 1):i283-91 12855471
16. GuhaThakurta D Stormo GD Identifying target sites for cooperatively binding factors Bioinformatics 2001, 17(7):608-21 11448879
17. Bailey TL Noble WS Searching for statistically significant regulatory modules Bioinformatics 2003, 19(Suppl 2):II16-II25 14534166
18. Frith MC Li MC Weng Z Cluster-Buster: Finding dense clusters of motifs in DNA sequences Nucleic Acids Res 2003, 31(13):3666-8 168947 12824389
19. Agrawal R Srikant R Mining sequential patterns Eleventh International Conference on Data Engineering (ICDE'95) 1995:3-14
20. Boulicaut JF Jeudy B Constraint-Based Data Mining The Data Mining and Knowledge Discovery Handbook Springer 2005
21. Sandve GK Drabløs F Generalized Composite Motif Discovery 7th Int Conf on Knowledge-Based Intelligent Information and Engineering Systems, KES LNCS/LNAI, Springer-Verlag 2005, 3683:763-769
22. Gordon DB Nekludova L McCallum S Fraenkel E TAMO: A flexible, object-oriented framework for analyzing transcriptional regulation using DNA-sequence motifs Bioinformatics 2005, 21(14):3164-5 15905282
23. Bailey TL Elkan C The value of prior knowledge in discovering motifs with MEME Proc Int Conf Intell Syst Mol Biol 1995, 3:21-9 7584439
24. Klepper K Sandve GK Abul O Johansen J Drablos F Assessment of composite motif discovery methods BMC Bioinformatics 2008, 9:123 2311304 18302777
25. Matys V Kel-Margoulis OV Fricke E Liebich I Land S Barre-Dirrie A Reuter I Chekmenev D Krull M Hornischer K Voss N Stegmaier P Lewicki-Potapov B Saxel H Kel AE Wingender E TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes Nucleic Acids Res 2006, 34 Database D108-10 1347505 16381825
26. Wasserman WW Fickett JW Identification of regulatory regions which confer muscle-specific gene expression J Mol Biol 1998, 278:167-81 9571041
27. Krivan W Wasserman WW A predictive model for regulatory sequences directing liver-specific transcription Genome Res 2001, 11(9):1559-66 311083 11544200
28. Ivan A Halfon M Sinha S Computational discovery of cis-regulatory modules in Drosophila without prior knowledge of motifs Genome Biol 2008, 9:R22 2395258 18226245
29. Gallo SM Li L Hu Z Halfon MS REDfly: A Regulatory Element Database for Drosophila Bioinformatics 2006, 22(3):381-383 16303794
30. Bryne JC Valen E Tang MH Marstrand T Winther O da Piedade I Krogh A Lenhard B Sandelin A JASPAR, the open access database of transcription factor-binding profiles: New content and tools in the 2008 update Nucleic Acids Res 2007, 36:D102-6 2238834 18006571
31. Sinha S van Nimwegen E Siggia ED A probabilistic method to detect regulatory modules Bioinformatics 2003, 19(Suppl 1):i292-301 12855472
32. Kel A Konovalova T Waleev T Cheremushkin E Kel-Margoulis O Wingender E Composite Module Analyst: A fitness-based tool for identification of transcription factor binding site combinations Bioinformatics 2006, 22(10):1190-7 16473870
33. Aerts S Van Loo P Thijs G Mayer H de Martin R Moreau Y De Moor B TOUCAN 2: The all-inclusive open source workbench for regulatory sequence analysis Nucleic Acids Res 2005, 33 Web Server W393-6 1160115 15980497
34. Grad YH Roth FP Halfon MS Church GM Prediction of similarly acting cis-regulatory modules by subsequence profiling and comparative genomics in Drosophila melanogaster and D. pseudoobscura Bioinformatics 2004, 20(16):2738-2750 15145800