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Database Commons - Shewanella knowledgebase

Shewanella knowledgebase

Citations: 12

z-index 0.00

Short name Shewanella knowledgebase
Full name
Description Integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions
URL http://spruce.ornl.gov:8080/Shewanella/
Year founded 2010
Last update & version 2010-01-01    v1.0
Availability Not Available
University/Institution hosted Oak Ridge National Laboratory
Address Oak Ridge, TN, USA
City Oak Ridge
Province/State TN
Country/Region United States
Contact name Tatiana V. Karpinets
Contact email karpinetstv@ornl.gov
Data type(s)
Major organism(s)
Keyword(s)
  • bioremediation
Publication(s)
  • Shewanella knowledgebase: integration of the experimental data and computational predictions suggests a biological role for transcription of intergenic regions. [PMID: 20627862]

    Tatiana V Karpinets, Margaret F Romine, Denise D Schmoyer, Guruprasad H Kora, Mustafa H Syed, Michael R Leuze, Margrethe H Serres, Byung H Park, Nagiza F Samatova, Edward C Uberbacher
    Database : the journal of biological databases and curation 2010:2010
    12 Citations (Google Scholar as of 2016-01-14)

    Abstract: Shewanellae are facultative gamma-proteobacteria whose remarkable respiratory versatility has resulted in interest in their utility for bioremediation of heavy metals and radionuclides and for energy generation in microbial fuel cells. Extensive experimental efforts over the last several years and the availability of 21 sequenced Shewanella genomes made it possible to collect and integrate a wealth of information on the genus into one public resource providing new avenues for making biological discoveries and for developing a system level understanding of the cellular processes. The Shewanella knowledgebase was established in 2005 to provide a framework for integrated genome-based studies on Shewanella ecophysiology. The present version of the knowledgebase provides access to a diverse set of experimental and genomic data along with tools for curation of genome annotations and visualization and integration of genomic data with experimental data. As a demonstration of the utility of this resource, we examined a single microarray data set from Shewanella oneidensis MR-1 for new insights into regulatory processes. The integrated analysis of the data predicted a new type of bacterial transcriptional regulation involving co-transcription of the intergenic region with the downstream gene and suggested a biological role for co-transcription that likely prevents the binding of a regulator of the upstream gene to the regulator binding site located in the intergenic region. Database URL: http://shewanella-knowledgebase.org:8080/Shewanella/ or http://spruce.ornl.gov:8080/Shewanella/

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Tags

DNA
Shewanella oneidensis
bioremediation

Record metadata

  • Created on: 2015-06-20
  • Curated by:
    • Lin Xia [2016-03-28]
    • Lin Xia [2015-06-28]
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