Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1

Shewanella oneidensis MR-1 is an important model organism for environmental research as it has an exceptional metabolic and respiratory versatility regulated by a complex regulatory network. We have developed a database to collect experimental and computational data relating to regulation of gene an...

Descripción completa

Detalles Bibliográficos
Autores principales: Syed, Mustafa H, Karpinets, Tatiana V, Leuze, Michael R, Kora, Guruprasad H, Romine, Margaret R, Uberbacher, Edward C
Formato: Texto
Lenguaje:English
Publicado: Biomedical Informatics Publishing Group 2009
Materias:
Database
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825598/
https://www.ncbi.nlm.nih.gov/pubmed/20198195
_version_ 1782177826909192192
author Syed, Mustafa H
Karpinets, Tatiana V
Leuze, Michael R
Kora, Guruprasad H
Romine, Margaret R
Uberbacher, Edward C
author_facet Syed, Mustafa H
Karpinets, Tatiana V
Leuze, Michael R
Kora, Guruprasad H
Romine, Margaret R
Uberbacher, Edward C
author_sort Syed, Mustafa H
collection PubMed
description Shewanella oneidensis MR-1 is an important model organism for environmental research as it has an exceptional metabolic and respiratory versatility regulated by a complex regulatory network. We have developed a database to collect experimental and computational data relating to regulation of gene and protein expression, and, a visualization environment that enables integration of these data types. The regulatory information in the database includes predictions of DNA regulator binding sites, sigma factor binding sites, transcription units, operons, promoters, and RNA regulators including non-coding RNAs, riboswitches, and different types of terminators. AVAILABILITY: http://shewanella-knowledgebase.org:8080/Shewanella/gbrowserLanding.jsp
format Text
id pubmed-2825598
institution National Center for Biotechnology Information
language English
publishDate 2009
publisher Biomedical Informatics Publishing Group
record_format MEDLINE/PubMed
spelling pubmed-28255982010-03-02 Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1 Syed, Mustafa H Karpinets, Tatiana V Leuze, Michael R Kora, Guruprasad H Romine, Margaret R Uberbacher, Edward C Bioinformation Database Shewanella oneidensis MR-1 is an important model organism for environmental research as it has an exceptional metabolic and respiratory versatility regulated by a complex regulatory network. We have developed a database to collect experimental and computational data relating to regulation of gene and protein expression, and, a visualization environment that enables integration of these data types. The regulatory information in the database includes predictions of DNA regulator binding sites, sigma factor binding sites, transcription units, operons, promoters, and RNA regulators including non-coding RNAs, riboswitches, and different types of terminators. AVAILABILITY: http://shewanella-knowledgebase.org:8080/Shewanella/gbrowserLanding.jsp Biomedical Informatics Publishing Group 2009-10-15 /pmc/articles/PMC2825598/ /pubmed/20198195 Text en © 2009 Biomedical Informatics Publishing Group This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.
spellingShingle Database
Syed, Mustafa H
Karpinets, Tatiana V
Leuze, Michael R
Kora, Guruprasad H
Romine, Margaret R
Uberbacher, Edward C
Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1
title Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1
title_full Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1
title_fullStr Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1
title_full_unstemmed Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1
title_short Shewregdb: Database and visualization environment for experimental and predicted regulatory information in Shewanella oneidensis mr-1
title_sort shewregdb: database and visualization environment for experimental and predicted regulatory information in shewanella oneidensis mr-1
topic Database
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2825598/
https://www.ncbi.nlm.nih.gov/pubmed/20198195
work_keys_str_mv AT syedmustafah shewregdbdatabaseandvisualizationenvironmentforexperimentalandpredictedregulatoryinformationinshewanellaoneidensismr1
AT karpinetstatianav shewregdbdatabaseandvisualizationenvironmentforexperimentalandpredictedregulatoryinformationinshewanellaoneidensismr1
AT leuzemichaelr shewregdbdatabaseandvisualizationenvironmentforexperimentalandpredictedregulatoryinformationinshewanellaoneidensismr1
AT koraguruprasadh shewregdbdatabaseandvisualizationenvironmentforexperimentalandpredictedregulatoryinformationinshewanellaoneidensismr1
AT rominemargaretr shewregdbdatabaseandvisualizationenvironmentforexperimentalandpredictedregulatoryinformationinshewanellaoneidensismr1
AT uberbacheredwardc shewregdbdatabaseandvisualizationenvironmentforexperimentalandpredictedregulatoryinformationinshewanellaoneidensismr1

Ejemplares similares