Promoter analysis of co-regulated genes in the yeast genome

Zhang, M. Q. (June 1999) Promoter analysis of co-regulated genes in the yeast genome. Computers & Chemistry, 23 (3-4). pp. 233-50. ISSN 0097-8485 (Print)

URL: http://www.ncbi.nlm.nih.gov/pubmed/10404618
DOI: 10.1016/S0097-8485(99)00020-0

Abstract

The use of high density DNA arrays to monitor gene expression at a genome-wide scale constitutes a fundamental advance in biology. In particular, the expression pattern of all genes in Saccharomyces cerevisiae can be interrogated using microarray analysis where cDNAs are hybridized to an array of more than 6000 genes in the yeast genome. In an effort to build a comprehensive Yeast Promoter Database and to develop new computational methods for mapping upstream regulatory elements, we started recently in an on going collaboration with experimental biologists on analysis of large-scale expression data. It is well known that complex gene expression patterns result from dynamic interacting networks of genes in the genetic regulatory circuitry. Hierarchical and modular organization of regulatory DNA sequence elements are important information for our understanding of combinatorial control of gene expression. As a bioinformatics attempt in this new direction, we have done some computational exploration of various initial experimental data. We will use cell-cycle regulated gene expression as a specific example to demonstrate how one may extract promoter information computationally from such genome-wide screening. Full report of the experiments and of the complete analysis will be published elsewhere when all the experiments are to be finished later in this year (Spellman, P.T., et al. 1998. Mol. Biol. Cell 9, 3273-3297).

Item Type: Paper
Uncontrolled Keywords: Base Sequence Cell Cycle/genetics DNA, Fungal/genetics Gene Expression Regulation, Fungal Genome, Fungal Histones/genetics Molecular Sequence Data Promoter Regions (Genetics) Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, P.H.S. Saccharomyces cerevisiae/cytology/ genetics
Subjects: organism description > yeast > Saccharomyces
organs, tissues, organelles, cell types and functions > cell types and functions > cell functions > cell cycle
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene expression
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > histone
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Kathleen Darby
Date: 15 June 1999
Date Deposited: 28 Apr 2014 14:04
Last Modified: 28 Apr 2014 14:04
Related URLs:
URI: http://repository.cshl.edu/id/eprint/29830

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