Towards accurate human promoter recognition: A review of currently used sequence features and classification methods

Briefings in Bioinformatics

Volumn 10, Issue 5, 2009, Pages 498-508

  Zeng, Jia ^a   Zhu, Shanfeng ^b   Yan, Hong ^c,d  

^a HONG KONG BAPTIST UNIVERSITY   (Hong Kong)

^b FUDAN UNIVERSITY   (China)

^c CITY UNIVERSITY OF HONG KONG   (Hong Kong)

^d UNIVERSITY OF SYDNEY   (Australia)

Author keywords

Feature extraction; Genome annotation; Human promoter recognition; Model selection

Indexed keywords

COMPLEMENTARY DNA; MESSENGER RNA;

ACCURACY; ALGORITHM; CLASSIFICATION; COMPUTER SYSTEM; CPG ISLAND; DNA SEQUENCE; EXPRESSED SEQUENCE TAG; GENE CONTROL; GENETIC DATABASE; GENETIC MODEL; GENOME; HUMAN; PROMOTER REGION; REVIEW;

GENE EXPRESSION REGULATION; GENOME, HUMAN; HUMANS; MODELS, GENETIC; PROMOTER REGIONS, GENETIC; PUBMED; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; TRANSCRIPTION INITIATION SITE;

EID: 69249146630     PISSN: 14675463     EISSN: 14774054     Source Type: Journal    
DOI: 10.1093/bib/bbp027     Document Type: Review

References (56)

1. Fickett JW, Hatzigeorgiou AG. Eukaryotic promoter recognition. Genome Res 1997;7:861-78.
2. Abeel T, Saeys Y, Bonnet E, et al. Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res 2008;18:310-23.
3. Zhang MQ. Computational analyses of eukaryotic promoters. BMC Bioinform 2007;8(Suppl. 6):S3.
4. Bajic VB, Brent MR, Brown RH, et al. Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol 2006; 7(Suppl. 1:S3):1-13.
5. Bajic VB, Tan SL, Suzuki Y, et al. Promoter prediction analysis on the whole human genome. Nat Biotechnol 2004;22:1467-73.
6. Werner T. The state of the art of mammalian promoter recognition. Brief Bioinform 2003;4:22-30.
7. Ohler U, Niemann H. Identification and analysis of eukaryotic promoters: recent computational approaches. Trends Genet 2001;17:56-60.
8. Pedersen AG, Baldi P, Chauvin Y, et al. The biology of eukaryotic promoter prediction - a review. Comput Chem 1999;23:191-207.
9. Smale ST, Kadonaga JT. The RNA polymerase II core promoter. Annu Rev Biochem 2003;72:449-79.
10. Gershenzon NI, Ioshikhes IP. Synergy of human Pol II core promoter elements revealed by statistical sequence analysis. Bioinformatics 2005;21:1295-300.
11. Takai D, Jones PA. Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci USA 2002;99:3740-5.
12. 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.
13. Fujii S, Kono H, Takenaka S, et al. Sequence-dependent DNA deformability studied using molecular dynamics simulations. Nucleic Acids Res 2007;35:6063-74.
14. Vardhanabhuti S, Wang J, Hannenhalli S. Position and distance specificity are important determinants of cis-regulatory motifs in addition to evolutionary conservation. Nucleic Acids Res 2007; 35:3203-13.
15. Tharakaraman K, Bodenreider O, Landsman D, et al. The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site. Nucleic Acids Res 2008;36:2777-86.
16. Fukue Y, Sumida N, Tanase J, et al. A highly distinctive mechanical property found in the majority of human promoters and its transcriptional relevance. Nucleic Acids Res 2005;33:3821-7.
17. Saxonov S, Berg P, Brutlag DL. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci USA 2006;103:1412-7.
18. Wang J, Ungar LH, Tseng H, et al. MetaProm: A neural network based meta-predictor for alternative human promoter prediction. BMC Genomics 2007;8:374.
19. Carninci P, Sandelin A, Lenhard B, et al. Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet 2006; 38:626-35.
20. Wang J, Hannenhalli S. A mammalian promoter model links cis elements to genetic networks. Biochem Biophys Res Commun 2006;347:166-77.
21. Wang X, Xuan Z, Zhao X, et al. High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res 2009;19:266-75.
22. Zhao X, Xuan Z, Zhang MQ. Boosting with stumps for predicting transcription start sites. Genome Biol 2007;8:R17.
23. Salton G, McGill MJ. Introduction to Modern Information Retrieval. New York: McGraw-Hill, 1983.
24. Wu S, Xie X, Liew AW, et al. Eukaryotic promoter prediction based on relative entropy and positional information. Phys Rev E Stat Nonlin Soft Matter Phys 2007; 75:041908.
25. Akan P, Deloukas P. DNA sequence and structural properties as predictors of human and mouse promoters. Gene 2008;410:165-76.
26. Pedersen AG, Baldi P, Chauvin Y, et al. DNA structure in human RNA polymerase II promoters. J Mol Biol 1998; 281:663-73.
27. Cao XQ, Zeng J, Yan H. Structural property of regulatory elements in human promoters. Phys Rev E Stat Nonlin Soft Matter Phys 2008; 77:041908.
28. Cao XQ, Zeng J, Yan H. Structural properties of replication origins in yeast DNA sequences. Phys Biol 2008;5:36012.
29. Ohler U, Niemann H, Liao G, et al. Joint modeling of DNA sequence and physical properties to improve eukaryotic promoter recognition. Bioinformatics 2001;17(Suppl. 1): S199-206.
30. Zeng J, Zhao X-Y, Cao X-Q, et al. SCS: Signal, context and structure features for genome-wide human promoter recognition. IEEE/ ACM Trans Comput Biol Bioinform 2009, doi:10.1109/TCBB.2008.95.
31. Goni JR, Perez A, Torrents D, et al. Determining promoter location based on DNA structure first-principles calculations. Genome Biol 2007;8:R263.
32. Abeel T, Saeys Y, Rouze P, et al. ProSOM: Core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics 2008;24:i24-31.
33. Packer MJ, Dauncey MP, Hunter CA. Sequence-dependent DNA structure: Tetranucleotide conformational maps. J Mol Biol 2000;295 85-103.
34. Mikkelsen TS, Ku M, Jaffe DB, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 2007; 448:553-560.
35. Burden S, Lin YX, Zhang R. Improving promoter prediction for the NNPP2.2 algorithm: A case study using Escherichia coli DNA sequences. Bioinformatics 2005; 21:601-7.
36. Davuluri RV, Grosse I, Zhang MQ. Computational identification of promoters and first exons in the human genome. Nat Genet 2001; 29:412-7.
37. Ponger L, Mouchiroud D. CpGProD: Identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics 2002;18: 631-3.
38. Down TA, Hubbard TJ. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res 2002;12:458-61.
39. Solovyev V, Kosarev P, Seledsov I, et al. Automatic annotation of eukaryotic genes, pseudogenes and promoters. Genome Biol 2006;7 (Suppl. 1):S1011-2.
40. Li X, Zeng J, Yan H. PCA-HPR: A principle component analysis model for human promoter recognition. Bioinformation 2008;2:373-8.
41. Knudsen S. Promoter2.0: For the recognition of PolII promoter sequences. Bioinformatics 1999;15:356-61.
42. Gangal R, Sharma P. Human pol II promoter prediction: Time series descriptors and machine learning. Nucleic Acids Res 2005;33 1332-6.
43. Bajic VB, Seah SH, Chong A, et al. Dragon Promoter Finder: recognition of vertebrate RNA polymerase II promoters. Bioinformatics 2002;18:198-9.
44. Bajic VB, Seah SH. Dragon gene start finder: An advanced system for finding approximate locations of the start of gene transcriptional units. Genome Res 2003;13: 1923-9.
45. Sonnenburg S, Zien A, Ratsch G. ARTS: Accurate recognition of transcription starts in human. Bioinformatics 2006;22: e472-80.
46. Xie X, Wu S, Lam KM, et al. PromoterExplorer: An effective promoter identification method based on the AdaBoost algorithm. Bioinformatics 2006;22:2722-8.
47. Won HH, Kim MJ, Kim S, et al. EnsemPro: An ensemble approach to predicting transcription start sites in human genomic DNA sequences. Genomics 2008;91:259-66.
48. Schmid CD, Perier R, Praz V, et al. EPD in its twentieth year: towards complete promoter coverage of selected model organisms. Nucleic Acids Res 2006;34:D82-5.
49. Flicek P, Aken BL, Beal K, et al. Ensembl 2008. Nucleic Acids Res 2008;36:D707-14.
50. Wakaguri H, Yamashita R, Suzuki Y, et al. DBTSS: Database of transcription start sites, progress report 2008. Nucleic Acids Res 2008;36:D97-101.
51. Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2007;35:D61-5.
52. Saxonov S, Daizadeh I, Fedorov A, et al. EID: The exon-intron database - an exhaustive database of protein-coding intron-containing genes. Nucleic Acids Res 2000;28:185-190.
53. Mignone F, Grillo G, Licciulli F, et al. UTRdb and UTRsite: A collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs. Nucleic Acids Res 2005;33 D141-6.
54. Wang X, Bandyopadhyay S, Xuan Z, et al. Prediction of transcription start sites based on feature selection using AMOSA. Comput Syst Bioinformatics Conf 2007;6:183-93.
55. Duda RO, Hart PE, Stork DG. Pattern Classification. New York: Wiley, 2001.
56. Chen X, Wu JM, Hornischer K, et al. TiProD: The tissue-specific promoter database. Nucleic Acids Res 2006;34: D104-7.