Identification of human gene core promoters in silico

Zhang, M. Q. (March 1998) Identification of human gene core promoters in silico. Genome Research, 8 (3). pp. 319-26. ISSN 1088-9051 (Print)

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URL: http://www.ncbi.nlm.nih.gov/pubmed/9521935
DOI: 10.1101/gr.8.3.319

Abstract

Identification of the 5'-end of human genes requires identification of functional promoter elements. In silico identification of those elements is difficult because of the hierarchical and modular nature of promoter architecture. To address this problem, I propose a new stepwise strategy based on initial localization of a functional promoter into a 1- to 2-kb (extended promoter) region from within a large genomic DNA sequence of 100 kb or larger and further localization of a transcriptional start site (TSS) into a 50- to 100-bp (corepromoter) region. Using positional dependent 5-tuple measures, a quadratic discriminant analysis (QDA) method has been implemented in a new program-CorePromoter. Our experiments indicate that when given a 1- to 2-kb extended promoter, CorePromoter will correctly localize the TSS to a 100-bp interval approximately 60% of the time. [Figure 3 can be found in its entirety as an online supplement at http://www.genome.org.]

Item Type: Paper
Uncontrolled Keywords: Analysis of Variance Computational Biology Genome, Human Humans Promoter Regions (Genetics)/ genetics Reproducibility of Results Research Support, U.S. Gov't, P.H.S. Sequence Analysis, DNA/ methods/statistics & numerical data Software
Subjects: bioinformatics > genomics and proteomics
bioinformatics > computational biology
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Kathleen Darby
Date: March 1998
Date Deposited: 30 Apr 2014 19:59
Last Modified: 30 Apr 2014 19:59
PMCID: PMC310696
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29942

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