CoryneRegNet 6.0: Updated database content, new analysis methods and novel features focusing on community demands

Josch Pauling, Richard Röttger, Andreas Tauch, Vasco Azevedo, Jan Baumbach

Research output: Contribution to journalJournal articleResearchpeer-review

Abstract

Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. The latter are genetic mechanisms that control a cell's characteristics, for instance, pathogenicity as well as survival and reproduction strategies. CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. Furthermore, with release 6.0, we provide easy-to-use functions that allow the user to submit data for persistent storage with the CoryneRegNet database. Thus, it offers important options to its users in terms of community demands. CoryneRegNet is publicly available at http://www.coryneregnet.de.
Original languageEnglish
JournalNucleic Acids Research
Volume40
Issue numberDatabase Issue
Pages (from-to)D610-4
ISSN0305-1048
DOIs
Publication statusPublished - 2012
Externally publishedYes

Fingerprint

Databases
Information Storage and Retrieval
Virulence

Cite this

@article{97086f72811d4c5aaa15f74c8956f791,
title = "CoryneRegNet 6.0: Updated database content, new analysis methods and novel features focusing on community demands",
abstract = "Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. The latter are genetic mechanisms that control a cell's characteristics, for instance, pathogenicity as well as survival and reproduction strategies. CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. Furthermore, with release 6.0, we provide easy-to-use functions that allow the user to submit data for persistent storage with the CoryneRegNet database. Thus, it offers important options to its users in terms of community demands. CoryneRegNet is publicly available at http://www.coryneregnet.de.",
author = "Josch Pauling and Richard R{\"o}ttger and Andreas Tauch and Vasco Azevedo and Jan Baumbach",
year = "2012",
doi = "10.1093/nar/gkr883",
language = "English",
volume = "40",
pages = "D610--4",
journal = "Nucleic Acids Research",
issn = "0305-1048",
publisher = "Heinemann",
number = "Database Issue",

}

CoryneRegNet 6.0 : Updated database content, new analysis methods and novel features focusing on community demands. / Pauling, Josch; Röttger, Richard; Tauch, Andreas; Azevedo, Vasco; Baumbach, Jan.

In: Nucleic Acids Research, Vol. 40, No. Database Issue, 2012, p. D610-4.

Research output: Contribution to journalJournal articleResearchpeer-review

TY - JOUR

T1 - CoryneRegNet 6.0

T2 - Updated database content, new analysis methods and novel features focusing on community demands

AU - Pauling, Josch

AU - Röttger, Richard

AU - Tauch, Andreas

AU - Azevedo, Vasco

AU - Baumbach, Jan

PY - 2012

Y1 - 2012

N2 - Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. The latter are genetic mechanisms that control a cell's characteristics, for instance, pathogenicity as well as survival and reproduction strategies. CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. Furthermore, with release 6.0, we provide easy-to-use functions that allow the user to submit data for persistent storage with the CoryneRegNet database. Thus, it offers important options to its users in terms of community demands. CoryneRegNet is publicly available at http://www.coryneregnet.de.

AB - Post-genomic analysis techniques such as next-generation sequencing have produced vast amounts of data about micro organisms including genetic sequences, their functional annotations and gene regulatory interactions. The latter are genetic mechanisms that control a cell's characteristics, for instance, pathogenicity as well as survival and reproduction strategies. CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. In this article we introduce the updated version 6.0 of CoryneRegNet and describe the updated database content which includes, 6352 corynebacterial regulatory interactions compared with 4928 interactions in release 5.0 and 3235 regulations in release 4.0, respectively. We also demonstrate how we support the community by integrating analysis and visualization features for transiently imported custom data, such as gene regulatory interactions. Furthermore, with release 6.0, we provide easy-to-use functions that allow the user to submit data for persistent storage with the CoryneRegNet database. Thus, it offers important options to its users in terms of community demands. CoryneRegNet is publicly available at http://www.coryneregnet.de.

U2 - 10.1093/nar/gkr883

DO - 10.1093/nar/gkr883

M3 - Journal article

VL - 40

SP - D610-4

JO - Nucleic Acids Research

JF - Nucleic Acids Research

SN - 0305-1048

IS - Database Issue

ER -