Development of Bioinformatic and Experimental Technologies for Identification of Prokaryotic Regulatory Networks

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The transcription regulatory network is arguably the most important foundation of cellular function, since it exerts the most fundamental control over the abundance of virtually all of a cell’s functional macromolecules. The two major components of a prokaryotic cell’s transcription regulation network are the transcription factors (TFs) and the transcription factor binding sites (TFBS); these components are connected by the binding of TFs to their cognate TFBS under appropriate environmental conditions. Comparative genomics has proven to be a powerful bioinformatics method with which to study transcription regulation on a genome-wide level. We have further extended comparative genomics technologies that we ... continued below

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9 pages

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Lawrence, Charles E & McCue, Lee Ann July 31, 2008.

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The transcription regulatory network is arguably the most important foundation of cellular function, since it exerts the most fundamental control over the abundance of virtually all of a cell’s functional macromolecules. The two major components of a prokaryotic cell’s transcription regulation network are the transcription factors (TFs) and the transcription factor binding sites (TFBS); these components are connected by the binding of TFs to their cognate TFBS under appropriate environmental conditions. Comparative genomics has proven to be a powerful bioinformatics method with which to study transcription regulation on a genome-wide level. We have further extended comparative genomics technologies that we introduced over the last several years. Specifically, we developed and applied statistical approaches to analysis of correlated sequence data (i.e., sequences from closely related species). We also combined these technologies with functional genomic, proteomic and sequence data from multiple species, and developed computational technologies that provide inferences on the regulatory network connections, identifying the cognate transcription factor for predicted regulatory sites. Arguably the most important contribution of this work emerged in the course of the project. Specifically, the development of novel procedures of estimation and prediction in discrete high-D settings has broad implications for biology, genomics and well beyond. We showed that these procedures enjoy advantages over existing technologies in the identification of TBFS. These efforts are aimed toward identifying a cell’s complete transcription regulatory network and underlying molecular mechanisms.

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9 pages

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  • Report No.: DOE/ER/63942-1
  • Grant Number: FG02-04ER63942
  • DOI: 10.2172/935264 | External Link
  • Office of Scientific & Technical Information Report Number: 935264
  • Archival Resource Key: ark:/67531/metadc897936

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Office of Scientific & Technical Information Technical Reports

Reports, articles and other documents harvested from the Office of Scientific and Technical Information.

Office of Scientific and Technical Information (OSTI) is the Department of Energy (DOE) office that collects, preserves, and disseminates DOE-sponsored research and development (R&D) results that are the outcomes of R&D projects or other funded activities at DOE labs and facilities nationwide and grantees at universities and other institutions.

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  • July 31, 2008

Added to The UNT Digital Library

  • Sept. 27, 2016, 1:39 a.m.

Description Last Updated

  • Nov. 4, 2016, 3:48 p.m.

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Lawrence, Charles E & McCue, Lee Ann. Development of Bioinformatic and Experimental Technologies for Identification of Prokaryotic Regulatory Networks, report, July 31, 2008; United States. (digital.library.unt.edu/ark:/67531/metadc897936/: accessed December 16, 2017), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.