Bioinformatic principles underlying the information content of transcription factor binding sites

Journal of Theoretical Biology

Volumn 220, Issue 4, 2003, Pages 529-544

  Kim, Jan T ^a   Martinetz, Thomas ^a   Polani, Daniel ^a  

^a Institut für Neuro und Bioinformatik   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; TRANSCRIPTION FACTOR;

BIOLOGY; GENETICS;

ANALYTIC METHOD; ARTICLE; BINDING SITE; BIOINFORMATICS; DNA BINDING; GENETIC CODE; GENOME; INFORMATION; MATHEMATICAL ANALYSIS; PRIORITY JOURNAL; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; THEORY;

EID: 0037458324     PISSN: 00225193     EISSN: None     Source Type: Journal    
DOI: 10.1006/jtbi.2003.3153     Document Type: Article

References (16)

1. BERG O. G., vON HIPPEL P. H. Selection of DNA binding sites by regulatory proteins. statistical-mechanical theory and application to operators and promoters. J. Mol. Biol. 193:1987;723-750.
2. COVER T. M., THOMAS J. A. Elements of Information Theory. 1991;John Wiley & Sons, New York.
3. FRECH K., QUANDT K., WERNER T. Software for the analysis of DNA sequence elements of transcription. Comput. Appl. Biosci. 13:1997;89-97.
4. JAYNES E. T. Information theory and statistical mechanics. Phys. Rev. 106:1952;620-630.
5. KAPPEN C., RUDDLE F. H. Evolution of a regulatory gene family: HOM/HOX genes. Curr. Opin. Genet. Develop. 3:1993;931-938.
6. KOLCHANOV N., PODKOLODNAYA O., ANANKO E., IGNATIEVA E., STEPANENKO I., KEL-MARGOULIS O., KEL A., MERKULOVA T., GORYACHKOVSKAYA T., BUSYGINA T., KOLPAKOV F., PODKOLODNY N., NAUMOCHKIN A., KOROSTISHEVSKAYA I., ROMASHCHENKO A., OVERTON G. Transcription regulatory regions database (TRRD): its status in 2000. Nucl. Acids Res. 28:2000;298-301.
7. PABO C. O., SAUER R. T. Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61:1992;1053-1095.
8. SCHMITT A. O., HERZEL H. Estimating the entropy of DNA sequences. J. theor. Biol. 1888:1997;369-377.
9. SCHNEIDER T. D. Evolution of biological information. Nucl. Acids Res. 28:2000;2794-2799.
10. SCHNEIDER T. D., STORMO G. D., GOLD L. Information content of binding sites on nucleotide sequences. J. Mol. Biol. 188:1986;415-431.
11. SHORE P., SHARROCKS A. D. The MADS-box family of transcription factors. Eur. J. Biochem. 229:1995;1-13.
12. STORMO G. D. Information content and free energy in DNA-protein interactions. J. theor. Biol. 195:1998;135-137.
13. STORMO G. D., FIELDS D. S. Specificity, free energy and information content in protein-DNA-interactions. Trends Biochem. Sci. 23:1998;109-113.
14. THEIßEN G., SAEDLER H. MADS-box genes in plant ontogeny and phylogeny: Haeckel's-"biogenetic law" revisited. Curr. Opin. Genetics Develop. 5:1995;628-639.
15. WINGENDER E., CHEN X., FRICKE E., GEFFERS R., HEHL R., LIEBICH I., KRULL M., MATYS V., MICHAEL H., OHNHÄUSER R., PRÜß M., SCHACHERER F., THIELE S., URBACH S. The TRANSFAC system on gene expression regulation. Nucl. Acids Res. 29:2001;281-283.
16. WU F. Y. The Potts model. Rev. Mod. Phys. 54:1982;235-268.