Searching for transcription factor binding sites in vector spaces

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Lee, Chih ^a   Huang, Chun Hsi ^a  

^a University of Connecticut   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AUTOMATIC OPTIMIZATION; COMPUTATIONAL APPROACH; CONSTRUCT QUERIES; CROSS VALIDATION; NOVEL METHODS; POSITION SPECIFIC SCORING MATRIX; SEARCH METHOD; SOURCE CODES; STATE-OF-THE-ART METHODS; TRANSCRIPTION FACTOR BINDING SITES;

BINDING SITES; OPTIMIZATION; QUERY PROCESSING; VECTOR SPACES;

TRANSCRIPTION FACTORS;

NUCLEOPOLYHEDROVIRUS;

TRANSCRIPTION FACTOR;

ALGORITHM; ANIMAL; ARTICLE; BINDING SITE; BIOLOGY; CHEMISTRY; COMPARATIVE STUDY; COMPUTER LANGUAGE; ESCHERICHIA COLI; GENETICS; HUMAN; METABOLISM; METHODOLOGY; MOUSE; POSITION WEIGHT MATRIX; PROTEIN BINDING; STATISTICAL MODEL;

ALGORITHMS; ANIMALS; BINDING SITES; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; HUMANS; LIKELIHOOD FUNCTIONS; MICE; POSITION-SPECIFIC SCORING MATRICES; PROGRAMMING LANGUAGES; PROTEIN BINDING; TRANSCRIPTION FACTORS;

MLCS; MLOWN;

EID: 84872170007     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-215     Document Type: Article

References (37)

1. Vilo J, Brazma A, Jonassen I, Robinson A, Ukkonen E. Mining for Putative Regulatory Elements in the Yeast Genome Using Gene Expression Data. Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology 2000, 384-394. San Diego, USA: AAAI Press.
2. Barash Y, Bejerano G, Friedman N. A Simple Hyper-Geometric Approach for Discovering Putative Transcription Factor Binding Sites. WABI '01: Proceedings of the First International Workshop on Algorithms in Bioinformatics 2001, 278-293. London, UK: Springer-Verlag, 2703950, 19417067.
3. Buhler J, Tompa M. Finding motifs using random projections. RECOMB '01: Proceedings of the fifth annual international conference on Computational biology 2001, 69-76. New York, NY, USA: ACM.
4. Sinha S. Discriminative motifs. RECOMB '02: Proceedings of the sixth annual international conference on Computational biology 2002, 291-298. New York, NY, USA: ACM.
5. Takusagawa KT, Gifford DK. Negative information for motif discovery. Pacific Symposium on Biocomputing 2004, 360-371. Big Island of Hawaii, USA: World Scientific.
6. Rajasekaran S, Balla S, Huang CH. Exact Algorithms for Planted Motif Problems. J Comput Biol 2005, 12(8):1117-1128. 10.1089/cmb.2005.12.1117, 16241901.
7. Balla S, Thapar V, Verma S, Luong T, Faghri T, Huang CHH, Rajasekaran S, del Campo JJ, Shinn JH, Mohler WA, Maciejewski MW, Gryk MR, Piccirillo B, Schiller SR, Schiller MR. Minimotif Miner: a tool for investigating protein function. Nat methods 2006, 3(3):175-177. 10.1038/nmeth856, 16489333.
8. Li N, Tompa M. Analysis of computational approaches for motif discovery. Algorithms for Mol Biol 2006, 1:8.
9. Zaslavsky E, Singh M. A combinatorial optimization approach for diverse motif finding applications. Algorithms for Mol Biol 2006, 1:13.
10. Yanover C, Singh M, Zaslavsky E. M are better than one: an ensemble-based motif finder and its application to regulatory element prediction. Bioinformatics 2009, 25(7):868-874. 10.1093/bioinformatics/btp090, 2660878, 19223448.
11. Georgiev S, Boyle A, Jayasurya K, Ding X, Mukherjee S, Ohler U. Evidence-ranked motif identification. Genome Biol 2010, 11(2):R19. 10.1186/gb-2010-11-2-r19, 2872879, 20156354.
12. 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 WSS, Pavesi G, Pesole G, Régnier 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, 23:137-144. 10.1038/nbt1053, 15637633.
13. Hu J, Li B, Kihara D. Limitations and potentials of current motif discovery algorithms. Nucleic Acids Res 2005, 33(15):4899-4913. 10.1093/nar/gki791, 1199555, 16284194.
14. Sandve G, Drablos F. A survey of motif discovery methods in an integrated framework. Biol Direct 2006, 1:11. 10.1186/1745-6150-1-11, 1479319, 16600018.
15. Staden R. Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res 1984, 12(1Part2):505-519. 10.1093/nar/12.1Part2.505, 321067, 6364039.
16. Schug J. Using TESS to Predict Transcription Factor Binding Sites in DNA Sequence. Curr Protoc Bioinf 2003, New York: J. Wiley and Sons, Baxevanis AD.
17. Kel A, Gößling E, Reuter I, Cheremushkin E, Kel-Margoulis O, Wingender E. MATCH™: a tool for searching transcription factor binding sites in DNA sequences. Nucleic Acids Res 2003, 31(13):3576-3579. 10.1093/nar/gkg585, 169193, 12824369.
18. Sandelin A, Wasserman WW, Lenhard B. ConSite: web-based prediction of regulatory elements using cross-species comparison. Nucleic Acids Res 2004, 32(suppl 2):W249-W252. 441510, 15215389.
19. Chekmenev DS, Haid C, Kel AE. P-Match: transcription factor binding site search by combining patterns and weight matrices. Nucleic Acids Res 2005, 33(suppl_2):W432-437. 1160202, 15980505.
20. Turatsinze JVV, Thomas-Chollier M, Defrance M, van Helden J. Using RSAT to scan genome sequences for transcription factor binding sites and cis-regulatory modules. Nat Protoc 2008, 3(10):1578-1588. 10.1038/nprot.2008.97, 18802439.
21. Zambelli F, Pesole G, Pavesi G. Pscan: finding over-represented transcription factor binding site motifs in sequences from co-regulated or co-expressed genes. Nucleic Acids Res 2009, 37(suppl 2):W247-W252. 2703934, 19487240.
22. Osada R, Zaslavsky E, Singh M. Comparative analysis of methods for representing and searching for transcription factor binding sites. Bioinformatics 2004, 20(18):3516-3525. 10.1093/bioinformatics/bth438, 15297295.
23. Salama RA, Stekel DJ. Inclusion of neighboring base interdependencies substantially improves genome-wide prokaryotic transcription factor binding site prediction. Nucleic Acids Res 2010, 38(12):e135. 10.1093/nar/gkq274, 2896541, 20439311.
24. Salton G, Wong A, Yang CS. A vector space model for automatic indexing. Commun ACM 1975, 18:613-620.
25. Lee DL, Chuang H, Seamons K. Document Ranking and the Vector-Space Model. IEEE Software 1997, 14:67-75.
26. Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muñiz-Rascado L, Martínez-Flores I, Salgado H, Bonavides-Martínez C, Abreu-Goodger C, Rodríguez-Penagos C, Miranda-Ríos J, Morett E, Merino E, Huerta AM, Treviño-Quintanilla L, Collado-Vides J. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res 2008, 36(suppl 1):D120-D124. 2238961, 18158297.
27. Portales-Casamar E, Thongjuea S, Kwon AT, Arenillas D, Zhao X, Valen E, Yusuf D, Lenhard B, Wasserman WW, Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res 2010, 38(suppl 1):D105-D110. 2808906, 19906716.
28. Bertsekas DP. Nonlinear Programming 1999, Belmont, MA: Athena Scientific.
29. Kroshko DL. OpenOpt 0.36. 2011, http://openopt.org/.
30. Fawcett T. An introduction to ROC analysis. Pattern Recogn Lett 2006, 27:861-874.
31. Wilcoxon F. Individual Comparisons by Ranking Methods. Biometrics Bulletin 1945, 1(6):80-83.
32. Hannenhalli S, Wang LS. Enhanced position weight matrices using mixture models. Bioinformatics 2005, 21(suppl_1):i204-212.
33. Georgi B, Schliep A. Context-specific independence mixture modeling for positional weight matrices. Bioinformatics 2006, 22(14):e166-e173. 10.1093/bioinformatics/btl249, 16873468.
34. de Hoon MJ, Imoto S, Nolan J, Miyano S. Open source clustering software. Bioinformatics 2004, 20(9):1453-1454. 10.1093/bioinformatics/bth078, 14871861.
35. Jain AK. Data clustering: 50 years beyond K-means. Pattern Recognit Lett 2010, 31(8):651-666.
36. Fujita PA, Rhead B, Zweig AS, Hinrichs AS, Karolchik D, Cline MS, Goldman M, Barber GP, Clawson H, Coelho A, Diekhans M, Dreszer TR, Giardine BM, Harte RA, Hillman-Jackson J, Hsu F, Kirkup V, Kuhn RM, Learned K, Li CH, Meyer LR, Pohl A, Raney BJ, Rosenbloom KR, Smith KE, Haussler D, Kent WJ. The UCSC Genome Browser database: update 2011. Nucleic Acids Res 2011, 39(suppl 1):D876-D882. 3242726, 20959295.
37. Rosenbloom KR, Dreszer TR, Pheasant M, Barber GP, Meyer LR, Pohl A, Raney BJ, Wang T, Hinrichs AS, Zweig AS, Fujita PA, Learned K, Rhead B, Smith KE, Kuhn RM, Karolchik D, Haussler D, Kent WJ. ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res 2010, 38(suppl 1):D620-D625. 2808953, 19920125.