Eukaryotic promoter recognition by binding sites for transcription factors
- PMID: 8590170
- DOI: 10.1093/bioinformatics/11.5.477
Eukaryotic promoter recognition by binding sites for transcription factors
Abstract
A method for identification of eukaryotic promoters by localization of binding sites for transcription factors has been suggested. The binding sites for a range of transcription factors have been found to be distributed unevenly. Based on these distributions, we have constructed a weight matrix of binding site localization. On the basis of the weight matrix we have, in turn, designed an algorithm for promoter recognition. To increase the accuracy of the method, we have developed a routine that breaks any promoter sample into subsamples. The method to be reported on allows much better recognition accuracy than does the approach based on detection of the TATA box. In particular, the overprediction error is three times lower following our method. The program FunSiteP recognizes promoters from newly uncovered sequences and tentatively identifies the functional class the promoters must belong to. We have introduced the notion of 'regulatory potential' for the degree to which any region of the sequences is similar to the real eukaryotic promoter. By making use of the potential, we have revealed putative transcription start sites and extended regions of transcription regulation.
Similar articles
-
Integrated databases and computer systems for studying eukaryotic gene expression.Bioinformatics. 1999 Jul-Aug;15(7-8):669-86. doi: 10.1093/bioinformatics/15.7.669. Bioinformatics. 1999. PMID: 10487874
-
Predicting Pol II promoter sequences using transcription factor binding sites.J Mol Biol. 1995 Jun 23;249(5):923-32. doi: 10.1006/jmbi.1995.0349. J Mol Biol. 1995. PMID: 7791218
-
Computer tool FUNSITE for analysis of eukaryotic regulatory genomic sequences.Proc Int Conf Intell Syst Mol Biol. 1995;3:197-205. Proc Int Conf Intell Syst Mol Biol. 1995. PMID: 7584437
-
X-ray crystallographic studies of eukaryotic transcription initiation factors.Philos Trans R Soc Lond B Biol Sci. 1996 Apr 29;351(1339):483-9. doi: 10.1098/rstb.1996.0046. Philos Trans R Soc Lond B Biol Sci. 1996. PMID: 8735270 Review.
-
The biology of eukaryotic promoter prediction--a review.Comput Chem. 1999 Jun 15;23(3-4):191-207. doi: 10.1016/s0097-8485(99)00015-7. Comput Chem. 1999. PMID: 10404615 Review.
Cited by
-
Logitlinear models for the prediction of splice sites in plant pre-mRNA sequences.Nucleic Acids Res. 1996 Dec 1;24(23):4709-18. doi: 10.1093/nar/24.23.4709. Nucleic Acids Res. 1996. PMID: 8972857 Free PMC article.
-
ARGO: a web system for the detection of degenerate motifs and large-scale recognition of eukaryotic promoters.Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W417-22. doi: 10.1093/nar/gki459. Nucleic Acids Res. 2005. PMID: 15980502 Free PMC article.
-
RBF-TSS: identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies.PLoS One. 2009;4(3):e4878. doi: 10.1371/journal.pone.0004878. Epub 2009 Mar 16. PLoS One. 2009. PMID: 19287502 Free PMC article.
-
Two splice variants of Golgi-microtubule-associated protein of 210 kDa (GMAP-210) differ in their binding to the cis-Golgi network.Biochem J. 2001 Aug 1;357(Pt 3):699-708. doi: 10.1042/0264-6021:3570699. Biochem J. 2001. PMID: 11463340 Free PMC article.
-
Organization and chromosomal localization of the human ECEL1 (XCE) gene encoding a zinc metallopeptidase involved in the nervous control of respiration.Biochem J. 2000 Mar 15;346 Pt 3(Pt 3):611-6. Biochem J. 2000. PMID: 10698686 Free PMC article.