skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Identification and characterization of transcription networks in environmentally significant species

Abstract

Understanding the regulation of gene expression, transcription regulation in particular, is one of the grand challenges of molecular biology. Transcription regulation is arguably the most important foundation of cellular function, since it exerts the most fundamental control of the abundance of virtually all of a cell's functional macromolecules. Nevertheless, this process, perhaps because of its difficulty, has been the subject of only a limited number of genomic level analyses. We have undertaken bioinformatics projects to address this issue by developing (1) a cross-species comparison method (i.e. phylogenetic footprinting) for the identification of transcription factor binding sites, (2) a Bayesian clustering method to identify regulons, (3) an improved scanning algorithm that uses a position weight matrix and several related species sequence data to locate transcription factor binding sites, and (4) a method to predict cognate binding sites for transcription factors of unknown specificity. These bioinformatics methods were developed using the model proteobacterium Escherichia coli, with further applications to the genomes of environmentally significant microbes (Rhodopseudomonas palustris, Shewanella oneidensis) in later years of the grant.

Authors:
;
Publication Date:
Research Org.:
Health Research Inc., Rensselaer, NY 12144
Sponsoring Org.:
USDOE Office of Science (SC); US - Atomic Energy Commission
OSTI Identifier:
860762
Report Number(s):
DOE/ER/63204-1
TRN: US200710%%173
DOE Contract Number:  
FG02-01ER63204
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; ABUNDANCE; ALGORITHMS; ESCHERICHIA COLI; FUNCTIONALS; GENES; MOLECULAR BIOLOGY; REGULATIONS; RHODOPSEUDOMONAS; SPECIFICITY; TRANSCRIPTION; TRANSCRIPTION FACTORS; bioinformatics; transcription regulation

Citation Formats

Lawrence, Charles E., and McCue, Lee Ann. Identification and characterization of transcription networks in environmentally significant species. United States: N. p., 2005. Web. doi:10.2172/860762.
Lawrence, Charles E., & McCue, Lee Ann. Identification and characterization of transcription networks in environmentally significant species. United States. doi:10.2172/860762.
Lawrence, Charles E., and McCue, Lee Ann. Wed . "Identification and characterization of transcription networks in environmentally significant species". United States. doi:10.2172/860762. https://www.osti.gov/servlets/purl/860762.
@article{osti_860762,
title = {Identification and characterization of transcription networks in environmentally significant species},
author = {Lawrence, Charles E. and McCue, Lee Ann},
abstractNote = {Understanding the regulation of gene expression, transcription regulation in particular, is one of the grand challenges of molecular biology. Transcription regulation is arguably the most important foundation of cellular function, since it exerts the most fundamental control of the abundance of virtually all of a cell's functional macromolecules. Nevertheless, this process, perhaps because of its difficulty, has been the subject of only a limited number of genomic level analyses. We have undertaken bioinformatics projects to address this issue by developing (1) a cross-species comparison method (i.e. phylogenetic footprinting) for the identification of transcription factor binding sites, (2) a Bayesian clustering method to identify regulons, (3) an improved scanning algorithm that uses a position weight matrix and several related species sequence data to locate transcription factor binding sites, and (4) a method to predict cognate binding sites for transcription factors of unknown specificity. These bioinformatics methods were developed using the model proteobacterium Escherichia coli, with further applications to the genomes of environmentally significant microbes (Rhodopseudomonas palustris, Shewanella oneidensis) in later years of the grant.},
doi = {10.2172/860762},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Nov 30 00:00:00 EST 2005},
month = {Wed Nov 30 00:00:00 EST 2005}
}

Technical Report:

Save / Share: