Prediction of human transcription regulatory motifs by using non-alignment based method

Progress in Biochemistry and Biophysics

Volumn 33, Issue 11, 2006, Pages 1044-1050

  Lü, Jun ^a,b   Luo, Liao Fu ^a   Zhang, Ying ^a,b   Zhao, Ju Dong ^a,b  

^a INNER MONGOLIA UNIVERSITY   (China)

^b INNER MONGOLIA UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Distance based conservative k mer searching algorithm; Non alignment based approach; Quadratic discriminant analysis; Transcription regulatory motifs

Indexed keywords

EID: 33947232194     PISSN: 10003282     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (24)

1. Taverner N V, Smith J C, Wardle F C. Identifying transcriptional targets. Genome Biology, 2004, 5 (3): 210.1-210.7
2. Wasserman W W, Sandelin A. Applied bioinformatics for the identification of regulatory elements. Nature Reviews Genetics, 2004, 5 (4): 276-287
3. Schena M, Shalon D, Davis R W, et al. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science, 1995, 270 (5235): 467-470
4. Shannon M F, Rao S. Transcription:Of chips and ChIPs. Science, 2002, 296 (5568): 666-669
5. van Steensel B, Henikoff S. Identification of in vivo DNA targets of chromatin proteins using tethered Dam methyltransferase. Nature Biotechnology, 2000, 18 (4): 424-428
6. Frith M C, Hansen U, Spouge J L, et al. Finding functional sequence elements by multiple local alignment. Nucleic Acids Research, 2004, 32 (1): 189-200
7. Pavesi G, Mereghetti P, Mauri G, et al. Weeder Web: discovery of transcription factor binding sites in a set of sequences from co-regulated genes. Nucleic Acids Research, 2004, 32(Web Server issue): W199-203
8. Blanchette M, Tompa M. Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Research, 2002, 12 (5): 739-748
9. Cliften P, Sudarsanam P, Desikan A, et al. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, 2003, 301 (5629): 71-76
10. Moses A M, Chiang D Y, Pollard D A, et al. MONKEY: identifying conserved transcription factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biology, 2004, 5 (12): R98.1-15
11. Chin C S, Chuang J H, Li H. Genome-wide regulatory complexity in yeast promoters: separation of functionally conserved and neutral sequence. Genome Research, 2005, 15 (2): 205-213
12. Bussemaker H J, Li H, Siggia E D. Regulatory element detection using correlation with expression. Nature Genetics, 2001, 27 (2): 167-171
13. Xie X, 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
14. Tompa M, Li N, Bailey T L, et al. Assessing computational tools for the discovery of transcription factor binding sites. Nature Biotechnology, 2005, 23 (1): 137-144
15. Elemento O, Tavazoie S. Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach. Genome Biology, 2005, 6 (2): R18.1-27
16. Matys V, Kel-Margoulis O V, Fricke E, et al. TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes. Nucleic Acids Research, 2006, 34 (Database issue): D108-110
17. Xuan Z, Zhao F, Wang J, et al. Genome-wide promoter extraction and analysis in human, mouse and rat. Genome Biology, 2005, 6 (8): R72.1-12
18. McLachlan G J. Discriminant analysis and statistical pattern recognition. New York :Wiley, 1992. 1-526
19. Zhang M Q.Identification of protein coding regions in the human genome by quadratic discriminant analysis. Proc Natl Acad Sci, 1997, 94 (2): 565-568
20. Zhang L R, Luo L F. Splice site prediction with quadratic discriminant analysis using diversity measure. Nucleic Acids Research, 2003, 31 (21): 6214-6220
21. Lu J, Luo L F. Prog Biochem Biophys, 2005, 32 (12): 1185-1191
22. Doniger S W, Huh J, Fay J C. Identification of functional transcription factor binding sites using closely related Saccharomyces Species. Genome Research, 2005, 15 (5): 701-709
23. Blanchette M, Bataille A R, Chen X, et al. Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Research, 2006, 16 (5): 656-668
24. FitzGerald P C, Shlyakhtenko A, Mir A A, et al. Clustering of DNA sequences in human promoters. Genome Research, 2004, 14 (8): 1562-1574