Pol II promoter prediction using characteristic 4-mer motifs: A machine learning approach

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Anwar, Firoz ^a   Baker, Syed Murtuza ^a   Jabid, Taskeed ^a   Mehedi Hasan, Md ^b   Shoyaib, Mohammad ^b   Khan, Haseena ^b   Walshe, Ray ^c  

^a EAST WEST UNIVERSITY   (Bangladesh)

^b UNIVERSITY OF DHAKA   (Bangladesh)

^c DUBLIN CITY UNIVERSITY   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

CLASSIFICATION MODELS; COMPUTATIONAL ANALYSIS; EUKARYOTIC ORGANISMS; EUKARYOTIC SEQUENCES; GENETIC REGULATORY NETWORKS; MACHINE LEARNING APPROACHES; PREDICTION AND ANALYSIS; PREDICTIVE PERFORMANCE;

FORECASTING; NUCLEIC ACIDS; RATS; SUPPORT VECTOR MACHINES; TOOLS;

LEARNING ALGORITHMS;

RNA POLYMERASE II; DROSOPHILA PROTEIN;

ACCURACY; ARTICLE; COMPUTER PREDICTION; DNA BINDING MOTIF; DNA SEQUENCE; FALSE POSITIVE RESULT; GENETIC ALGORITHM; PROMOTER REGION; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS; SUPPORT VECTOR MACHINE; TATA BOX; ANIMAL; ARTIFICIAL INTELLIGENCE; CONFORMATION; EUKARYOTIC CELL; GENETICS; GENOMICS; HUMAN; METHODOLOGY; MOUSE; NUCLEIC ACID DATABASE; RAT; REPRODUCIBILITY; STRUCTURE ACTIVITY RELATION;

EUKARYOTA; RATTUS;

ANIMALS; ARTIFICIAL INTELLIGENCE; DATABASES, NUCLEIC ACID; DROSOPHILA PROTEINS; EUKARYOTIC CELLS; GENOMICS; HUMANS; MICE; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS, GENETIC; RATS; REPRODUCIBILITY OF RESULTS; RNA POLYMERASE II; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 55049130233     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-414     Document Type: Article

References (34)

1. Bucher P Weight rr matrix description of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences J Mol Biol 1990, 212:563-578. 2329577
2. Fickett JW Hatzigeorgiou AC Eukaryotic promoter recognition Genome Res 1997, 7:861-878. 9314492
3. Zhang MQ Identification of Human Gene Core Promoters in Silico Genome Research 1998, 8:319-326. 310696 9521935
4. Ohler U Harbeck S Niemann H Noth E Reese M Interpolated Markov chains for eukaryotic promoter recognition Bioinformatics 1999, 15:362-369. 10366656
5. Uwe O Identification of core promoter modules in Drosophila and their application in accurate transcription start site prediction Nucleic Acids Res 2006, 34:5943-5950. 1635271 17068082
6. Chin YL Santoso B Boulay T Dong E Ohler U Kadonaga JT The MTE, a new core promoter element for transcription by RNA polymerase II Genes and Dev 2004, 18:1606-1617.
7. Knudsen S Promoter 2.0: For recognition of Pol II promoter sequences Biotechnologies 1999, 15:356-361.
8. Pandey SP Krishnamachari A Computational analysis of plant RNA Pol-II promoters Bio Systems 2006, 83:38-50. 16236422
9. Scherf M Klingenhoff A Frech K Qu TK Schneider R Grote K Frisch M Gailus-Durner V Seidel A Brack-Werner R Werner T First pass annotation of promoters of human chromosome 22 Genome Res 2001, 11:333-340. 311038 11230158
10. Davuluri VR Grosse I Zhang MQ Computational identification of promoters and first exons in the human genome Nature Genetics 2001, 29:412-417. 11726928
11. Bajic VB Seah SH Chong A Zhang G Koh JLY Brusic V Dragon promoter finder: Recognition of vertebrate RNA polymerase II promoters Bioinformatics 2002, 18:198-199. 11836231
12. Dragon Promoter Finder 1.5
13. Reese M Harris NL Eeckman FH Large scale sequencing specific neural networks for promoter and splice site recognition Biocomputing Proceedings of the 1996 Pacific Symposium World Scientific Co Hunter L, Klein T 1996.
14. NNP 2.2 http://www.fruitfly.org/seq_tools/promoter.html
15. Reese MG Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome Computers and Chemistry 2001, 26:51-56.
16. Prom 2 http://www.cbs.dtu.dk/services/Promoter/
17. Scherf M Klingenhoff A Werner T Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: A novel context analysis approach J Mol Biol 2000, 297:599-606. 10731414
18. Down TA Hubbard TJ Computational detection and location of transcription start sites in mammalian genomic DNA Genome Res 2002, 12:458-461. 155284 11875034
19. Xiao-Tu M Min-Ping Q Hai-Xu T Predicting Polymerase II Core Promoters by Cooperating Transcription Factor Binding Sites in Eukaryotic Genes Acta Biochimica et Biophysica Sinica 2004, 36:250-258. 15253150
20. Rajeev G Pankaj S Human pol II promoter prediction: Time series descriptors and machine learning Nucleic Acids Res 2005, 33:1332-1336. 552959 15741185
21. Shahmuradov IA Solovyev VV Gammerman AJ Plant promoter prediction with confidence estimation Nucleic Acids Research 2005, 33:1069-1076. 549412 15722481
22. Gershenzon N Ioshikhes I Synergy of human Pol II core promoter elements revealed by statistical sequence analysis Bioinformatics 2005, 21:1295-1300. 15572469
23. Jin V Singer G Davuluri R Genome-wide Analysis of Core Promoters from Conserved Human and Mouse Orthologous Pairs BMC Bioinformatics 2006, 7:114. 1475891 16522199
24. Hutchinson G The prediction of vertebrate promoter regions using differential hexamer frequency analysis Bioinformatics 1996, 12(5):391-398.
25. Chan B Kibler D Using hexamers to predict cis-regulatory motifs in Drosophila BMC Bioinformatics 2005, 6:262. 1291357 16253142
26. Ohler U Liao G Niemann H Rubin G Computational analysis of core promoters in the Drosophila genome Genome Biol 2002, 3:1-12.
27. Shahmuradov I Gammerman A Hancock JM Bramley PM Solovyev VV PlantProm: A database of plant promoter sequences Nucleic Acids Res 2003, 31:114-117. 165488 12519961
28. Zhang M A discrimination study of human core-promoters Pac Symp Biocomput 1998:307-309.
29. Hardison R Comparative Genomics PLoS Biol 2003, 1:E58. 261895 14624258
30. EPD http://www.epd.isb-sib.ch/
31. Schmid C Perier R Praz V Bucher P EPD in its twentieth year: Towards complete promoter coverage of selected model organisms Nucleic Acids Res 2006, 34:D82-D85. 1347508 16381980
32. Boser BE Guyon IM Vapnik VN A training algorithm for optimal margin classifiers Proceedings of the 5th Annual ACM Workshop on Computational Learning Theory ACM Press 1992:144-152.
33. Chih-Wei H Chih-Chung C Chih-Jen L A Practical Guide to Support Vector Classification National Taiwan University 2004.
34. Bradley E Gail G A Leisurely Look at the Bootstrap, the Jackknife, and Cross-Validation The American Statistician 1983, 37(1):36-48.