Automatic transcription factor classifier based on functional domain composition

Biochemical and Biophysical Research Communications

Volumn 347, Issue 1, 2006, Pages 141-144

  Qian, Ziliang ^a,b   Cai, Yu Dong ^a,c   Li, Yixue ^a,d  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c UNIVERSITY OF MANCHESTER   (United Kingdom)

^d SHANGHAI CENTER FOR BIOINFORMATION TECHNOLOGY   (China)

Author keywords

Functional domain composition; Intimate sorting classifier; Jackknife cross validation test; Transcription factors

Indexed keywords

HELIX LOOP HELIX PROTEIN; SCAFFOLD PROTEIN; TRANSCRIPTION FACTOR; ZINC;

ARTICLE; DNA PROTEIN COMPLEX; EUKARYOTE; GENE CONTROL; NONHUMAN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN FUNCTION; TRANSCRIPTION REGULATION; VALIDATION PROCESS;

ARTIFICIAL INTELLIGENCE; BINDING SITES; CLUSTER ANALYSIS; DATABASES, PROTEIN; PATTERN RECOGNITION, AUTOMATED; PROTEIN BINDING; PROTEIN INTERACTION MAPPING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; STRUCTURE-ACTIVITY RELATIONSHIP; TRANSCRIPTION FACTORS;

EUKARYOTA;

EID: 33745752255     PISSN: 0006291X     EISSN: 10902104     Source Type: Journal    
DOI: 10.1016/j.bbrc.2006.06.060     Document Type: Article

References (18)

1. Chou K.C., and Cai Y.D. Using functional domain composition and support vector machines for prediction of protein subcellular location. J. Biol. Chem. 277 (2002) 45765-45769
2. Matys V., Kel-Margoulis O.V., Fricke E., Liebich I., Land S., Barre-Dirrie A., Reuter I., Chekmenev D., Krull M., Hornischer K., Voss N., Stegmaier P., Lewicki-Potapov B., Saxel H., Kel A.E., and Wingender E. TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes. Nucleic Acids Res. 34 (2006) D108-D110
3. Matys V., Fricke E., Geffers R., Gossling E., Haubrock M., Hehl R., Hornischer K., Karas D., Kel A.E., Kel-Margoulis O.V., Kloos D.U., Land S., Lewicki-Potapov B., Michael H., Munch R., Reuter I., Rotert S., Saxel H., Scheer M., Thiele S., and Wingender E. TRANSFAC(R): transcriptional regulation, from patterns to profiles. Nucleic Acids Res. 31 (2003) 374-378
4. Wingender E. Classification scheme of eukaryotic transcription factors Molekularnaya. Biologiya 31 (1997) 483-497
5. Wojcik J., and Schachter V. Protein-protein interaction map inference using interacting domain profile pairs. Bioinformatics 17 (2001) S296-S305
6. Chou K.C., and Cai Y.D. Predicting protein structural class by functional domain composition. Biochem. Biophys. Res. Commun. 321 (2004) 1007-1009
7. Cai Y.D., and Chou K.C. Predicting enzyme subclass by functional domain composition and pseudo amino acid composition. J. Proteome Res. 4 (2005) 967-971
8. Cai Y.D., and Doig A.J. Prediction of Saccharomyces cerevisiae protein functional class from functional domain composition. Bioinformatics 20 (2004) 1292-1300
9. Yu X.J., Lin J.C., Shi T.L., and Li Y.X. A novel domain-based method for predicting the functional classes of proteins. Chinese Sci. Bull. 49 (2004) 2379-2384
10. Li W., Jaroszewski L., and Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics 18 (2002) 77-82
11. Li W., Jaroszewski L., and Godzik A. Clustering of highly homologous sequences to reduce the size of large protein databases. Bioinformatics 17 (2001) 282-283
12. Wang G., and Dunbrack Jr. R.L. PISCES: a protein sequence culling server. Bioinformatics 19 (2003) 1589-1591
13. Zhou G.P. An intriguing controversy over protein structural class prediction. J. Protein Chem. 17 (1998) 729-738
14. Chou K.C. A novel approach to predicting protein structural classes in a (20-1)-D amino acid composition space. Proteins: Struct. Funct. Genet. 21 (1995) 319-344
15. Cai Y.D., and Chou K.C. Predicting membrane protein type by functional domain composition and pseudo-amino acid composition. J. Theor. Biol. 238 (2006) 395-400
16. Cai Y.D., and Chou K.C. Predicting membrane protein type by functional domain composition and pseudo-amino acid composition. J. Theor. Biol. 238 (2006) 395-400
17. Yu X., Wang C., and Li Y. Classification of protein quaternary structure by functional domain composition BMC. Bioinformatics 7 (2006) 187
18. Luscombe N.M., Austin S.E., Helen M., and Thornton J.M. An overview of the structures of protein-DNA complexes. Genome Biol. 1 (2000) reviews 001