title: Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet.
abstract: 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.
authors.affiliation: Algorithms Group, International Computer Science Institute, Berkeley, California, USA. jbaumbac@icsi.berkeley.edu
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
authors.forename: Tobias
authors.initials: T
authors.lastname: Wittkop
authors.forename: Christiane Katja
authors.initials: CK
authors.lastname: Kleindt
authors.forename: Andreas
authors.initials: A
authors.lastname: Tauch
mesh_terms: D019295:Computational Biology / Q000379:methods*; D003352:Corynebacterium / Q000235:genetics*; D030541:Databases, Genetic; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D020407:Internet; D014157:Transcription Factors / Q000235:genetics; D014158:Transcription, Genetic; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors