Human pol II promoter prediction

Progress in Biochemistry and Biophysics

Volumn 32, Issue 12, 2005, Pages 1185-1191

  Lü, Jun ^a,b   Luo, Liao Fu ^a  

^a INNER MONGOLIA UNIVERSITY   (China)

^b INNER MONGOLIA UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Increment of diversity; Promoter; Quadratic discriminant analysis; Transcription start site

Indexed keywords

EID: 33644686177     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (30)

1. Fickett J W. Finding genes by computer: The state of the art. Trends Genet, 1996, 12 (8): 316-320
2. Gelfand M S. Prediction of function in DNA sequence analysis. J Comp Biol, 1995, 2 (1): 87-115
3. Bucher P. Weight matrix description of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol, 1990, 212 (4): 563-578
4. Fickett J W, Hatzigeorgiou A C. Eukaryotic promoter recognition. Genome Res, 1997, 7 (9): 861-878
5. Knudsen S. Promoter 2.0: for recognition of Pol II promoter sequences. Bioinformatics, 1999, 15 (5): 356-361
6. Bajic V B, Seah S H, Chong A, et al. Dragon promoter finder: recognition of vertebrate RNA polymerase II promoters. Bioinformatics, 2002, 18 (1): 198-199
7. Lemon B, Tjian R. Orchestrated response: a symphony of transcription factors for gene control. Genes Dev, 2000, 14 (20): 2551-2569
8. Pedersen A G, Baldi P, Chauvin Y, et al. The biology of eukaryotic promoter prediction-a review. Comput Chem, 1999, 23(3-4): 191-207
9. Smale S T. Transcription initiation from TATA-less promoters within eukaryotic protein-coding genes. Biochim Biophys Acta, 1997, 1351 (1-2): 73-88
10. Smale S T. Core promoters: active contributors to combinatorial gene regulation. Genes Dev, 2001, 15 (19): 2503-2508
11. Werner T. Models for prediction and recognition of eukaryotic promoters. Mamm Genome, 1999, 10 (2): 168-175
12. Wasserman W W, Palumbo M, Thompson W, et al. Human-mouse genome comparisons to locate regulatory sites. Nature Genet, 2000, 26 (2): 225-228
13. Solovyev V, Salamov A. The Gene-Finder computer tools for analysis of human and model organisms genome sequences. Proc Int Conf Intell Syst Mol Biol, 1997, 5: 294-302
14. Gangal R, Sharma P. Human pol II promoter prediction: time series descriptors and machine learning. Nucleic Acids Research, 2005, 33(4): 1332-1336
15. Zhang MQ. Identification of human gene core promoters in silico. Genome Res, 1998, 8 (3): 319-326
16. Davuluri R V, Grosse I, Zhang M Q. Computer identification of promoters and first exons in the human genome. Nature Genetics, 2001, 29 (4): 412-417
17. Reese M G. Application of a time-delay neural network to promoter annotation in the Drosophila melanogaster genome. Comput Chem, 2001, 26(1): 51-56
18. Prestridge D S. Predicting Pol II promoter sequences using transcription factor binding sites. J Mol Biol, 1995, 249 (5): 923-932
19. Shahmuradov I A, Solovyev V V, Gammerman A J. Plant promoter prediction with confidence estimation. Nucleic Acids Research, 2005, 33(3): 1069-1076
20. Roeder R G. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem Sci, 1996, 21 (9): 327-335
21. Xie X H, Lu J, Kulbokas E J, et al. Systematic discovery of regulatory motifs in human promoters and 3'UTRs by comparison of several mammals. Nature, 2005, 434 (7031): 338-345
22. Laxton R R. The measure of diversity. J Theor Biol, 1978, 71(1): 51-67
23. McLachlan G J. Discriminant Analysis and Statistical Pattern Recognition. New York: Wiley, 1992. 1-526
24. Zhang M Q. Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc Natl Acad Sci USA, 1997, 94 (2): 565-568
25. Zhang L R, Luo L F. Splice site prediction with quadratic discriminant analysis using diversity measure. Nucleic Acids Research, 2003, 31(21): 6214-6220
26. Schmid C D, Praz V, Delorenzi M, et al. The eukaryotic promoter database EPD: the impact of in silico primer extension. Nucleic Acids Research, 2004, 32: D82-85
27. Matthias S, Andreas K, Kornelie F, et al. First pass annotation of promoters on human chromosome 22. Genome Res, 2001, 11(3): 333-340
28. Luo L F, Li H, Zhang L R. ORF organization and gene recognition in the yeast genome. Comp Funct Genomics, 2003, 4 (3): 318-328
29. Suzuki Y, Yamashita R, Sugano S, et al. DBTSS, DataBase of transcriptional start sites: progress report 2004. Nucleic Acids Research, 2004, 32: D78-D81
30. Suzuki Y, Taira H, Tsunoda T, et al. Diverse transcriptional initiation revealed by fine, large-scale mapping of mRNA start sites. EMBO Rep, 2001, 2 (5): 388-393