title: Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.
abstract: To handle changing environmental surroundings and to manage unfavorable conditions, microbial organisms have evolved complex transcriptional regulatory networks. To comprehensively analyze these gene regulatory networks, several online available databases and analysis platforms have been implemented and established. In this article, we address the typical cycle of scientific knowledge exploration and integration in the area of procaryotic transcriptional gene regulation. We briefly review five popular, publicly available systems that support (i) the integration of existing knowledge, (ii) visualization capabilities and (iii) computer analysis to predict promising wet lab targets. We exemplify the benefits of such integrated data analysis platforms by means of four application cases exemplarily performed with the corynebacterial reference database CoryneRegNet.
authors.affiliation: International Computer Science Institute, Berkeley, USA. jbaumbac@icsi.berkeley.edu
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
authors.forename: Andreas
authors.initials: A
authors.lastname: Tauch
authors.forename: Sven
authors.initials: S
authors.lastname: Rahmann
mesh_terms: D000085:Acetates / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D003352:Corynebacterium / Q000235:genetics* / Q000378:metabolism; D003628:Database Management Systems; D030541:Databases, Genetic; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D016680:Genome, Bacterial; D005947:Glucose / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D000085:Acetates; D001426:Bacterial Proteins; D005947:Glucose