Comparative Analysis of Transcription Start Sites Using Mutual Information

Genomics, Proteomics and Bioinformatics

Volumn 4, Issue 3, 2006, Pages 189-195

  Reddy, D Ashok ^a   Mitra, Chanchal K ^a  

^a UNIVERSITY OF HYDERABAD   (India)

Author keywords

information content; substitution matrices; transcription start site (TSS)

Indexed keywords

DINUCLEOTIDE;

COMPARATIVE STUDY; ESCHERICHIA COLI; HUMAN; INFORMATION; LETTER; MITOCHONDRION; NONHUMAN; PROMOTER REGION; TRANSCRIPTION INITIATION SITE;

ESCHERICHIA COLI;

EID: 33751230751     PISSN: 16720229     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1672-0229(06)60032-6     Document Type: Article

References (28)

1. Smale S.T., and Kadonaga J.T. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72 (2003) 449-479
2. Taanman J.W. The mitochondrial genome: structure, transcription, translation and replication. Biochim. Biophys. Acta 1410 (1999) 103-123
3. Boore J.L. Animal mitochondrial genomes. Nucleic Acids Res. 27 (1999) 1767-1780
4. Montoya J., et al. Identification of initiation sites for heavy-strand and light-strand transcription in human mitochondrial DNA. Proc. Natl. Acad. Sci. USA 79 (1982) 7195-7199
5. Dayhoff M.O., et al. A model of evolutionary change in proteins. In: Dayhoff M.O. (Ed). Atlas of Protein Sequence and Structure Volume 5 (1978), National Biomedical Research Foundation, Washington DC, USA 345-352
6. Schwartz R.M., and Dayhoff M.O. Matrices of detecting distant relationship. In: Dayhoff M.O. (Ed). Atlas of Protein Sequence and Structure Volume 5 (1978), National Biomedical Research Foundation, Washington DC, USA 353-358
7. Henikoff S., and Henikoff J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. USA 89 (1992) 10915-10919
8. Gonnet G.H., et al. Exhaustive matching of the entire protein sequence database. Science 256 (1992) 1443-1445
9. Lunter G., and Hein J. A nucleotide substitution model with nearest-neighbour interactions. Bioinformatics 20 (2004) 1216-1223
10. Arndt P.F., and Hwa T. Identification and measurement of neighbor-dependent nucleotide substitution processes. Bioinformatics 21 (2005) 2322-2328
11. Reddy D.A., et al. Comparative analysis of core promoter region: information content from mono and dinucleotide substitution matrices. Comput. Biol. Chem. 30 (2006) 58-62
12. Gershenzon N.I., et al. Computational technique for improvement of the position-weight matrices for the DNA/protein binding sites. Nucleic Acids Res. 33 (2005) 2290-2301
13. Bulyk M.L., et al. Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors. Nucleic Acids Res. 30 (2002) 1255-1261
14. Reddy D.A., et al. Functional classification of transcription factor binding sites: information content as a metric. J. Integr. Bioinformatics 3 (2006) 20
15. Bajic V.B., et al. Content analysis of the core promoter region of human genes. In Silico Biol. 4 (2004) 109-125
16. Aerts S., et al. Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics 5 (2004) 34
17. Bucher P. Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J. Mol. Biol. 212 (1990) 563-578
18. Down T.A., and Hubbard T.J. Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 12 (2002) 458-461
19. Martin L.C., et al. Using information theory to search for co-evolving residues in proteins. Bioinformatics 21 (2005) 4116-4124
20. Dawy Z., et al. Gene mapping and marker clustering using Shannon's mutual information. IEEE/ACM Trans. Comput. Biol. Bioinform. 3 (2006) 47-56
21. Leitao H.C., et al. Mutual information content of homologous DNA sequences. Genet. Mol. Res. 4 (2005) 553-562
22. Chang C.H., et al. Shannon information in complete genomes. J. Bioinform. Comput. Biol. 3 (2005) 587-608
23. Shannon C.E. A mathematical theory of communication. Bell Syst. Tech. J. 27 (1948) 379-423 623-656.
24. Cover T.M., and Thomas J.A. Elements of Information Theory (1991), John Wiley & Sons, New York, USA
25. Périer R.C., et al. The Eukaryotic Promoter Database EPD. Nucleic Acids Res. 26 (1998) 353-357
26. Hershberg R., et al. PromEC: an updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Nucleic Acids Res. 29 (2001) 277
27. Karlin S., and Altschul S.F. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl. Acad. Sci. USA 87 (1990) 2264-2268
28. Altschul S.F. Amino acid substitution matrices from an information theoretic perspective. J. Mol. Biol. 219 (1991) 555-565