Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet

被引：32

作者：

Baumbach, Jan ^{[1
]}

Wittkop, Tobias ^{[1
,2
,3
]}

Kleindt, Christiane Katja ^{[2
,4
]}

Tauch, Andreas ^{[5
]}

机构：

[1] Int Comp Sci Inst, Algorithms Grp, Berkeley, CA 94704 USA

[2] Univ Bielefeld, Int Grad Sch Bioinformat & Genome Res, Bielefeld, Germany

[3] Univ Bielefeld, Grad Kolleg Bioinformat, Bielefeld, Germany

[4] Univ Calif Berkeley, Dept Plant & Microbial Biol, Berkeley, CA 94720 USA

[5] Univ Bielefeld, Inst Genome Res & Syst Biol, Ctr Biotechnol, Bielefeld, Germany

来源：

NATURE PROTOCOLS | 2009年 / 4卷 / 06期

关键词：

COMPLETE GENOME SEQUENCE; ESCHERICHIA-COLI K-12; OPERON ORGANIZATION; BACILLUS-SUBTILIS; CORYNEBACTERIUM-GLUTAMICUM; REGULONDB; DATABASE; GROWTH; DBTBS; PROMOTERS;

D O I：

10.1038/nprot.2009.81

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

CoryneRegNet is the reference database and analysis platform for corynebacterial gene regulatory networks. It provides web-based access to integrated data on gene regulatory interactions of corynebacteria relevant to human medicine and biotechnology, Escherichia coli and Mycobacterium tuberculosis. To facilitate the analysis and reconstruction of the corresponding networks, CoryneRegNet provides user-friendly interfaces for bioinformatics analysis and network visualization tools. This protocol describes four major workflows: (1) querying the regulatory network of a gene of interest, (2) prediction and interspecies transfer of gene regulatory interactions, (3) visualization and comparison of predicted or known networks and (4) integration of gene expression data analysis and visualization. This protocol guides the user through the most important features of CoryneRegNet and takes 45-60 min to complete.

引用

页码：992 / 1005

页数：14

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