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.

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Figure 1: Overview of the CoryneRegNet user interface.
Figure 2: Details page for the global iron-dependent repressor protein DtxR of Corynebacterium glutamicum.
Figure 3: Visualization of the gene regulatory network of DtxR with GraphVis.
Figure 4: Prediction of GlxR transcription factor binding sites—network transfer from Corynebacterium glutamicum to Corynebacterium jeikeium.

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Acknowledgements

J.B. thanks the German Academic Exchange Service (DAAD) for funding his work at ICSI, Berkeley. T.W. is grateful for financial support of the International Graduate School for Bioinformatics and Genome Research (IGS, Bielefeld, Germany) and the Boehringer Ingelheim Fonds. C.K.K. thanks the IGS as well as the Arabidopsis Functional Genomics network (AFGN)—2010 Young Researcher Exchange Program for funding her work at UC Berkeley.

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Correspondence to Jan Baumbach.

Supplementary information

Supplementary Data 1: Sample transcription factor binding sites (15 arbitrarily selected) for DtxR of Corynebacterium glutamicum as text file in FASTA format.

This text file contains 15 arbitrarily selected binding sites of DtxR in FASTA format. They are used as input for the TFBScan feature in Step 2D of the protocol. (TXT 0 kb)

Supplementary Data 2: Sample DtxR knock-out gene expression data for Corynebacterium glutamicum as tab-delimited flat-file.

This text file contains all significantly differentially expressed genes and M-values for a DtxR knock-out microarray experiment43. The gene IDs and M-values are stored tab-delimited, one line for each pair. This file is used in Step 2E of the protocol. (TXT 3 kb)

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Baumbach, J., Wittkop, T., Kleindt, C. et al. Integrated analysis and reconstruction of microbial transcriptional gene regulatory networks using CoryneRegNet. Nat Protoc 4, 992–1005 (2009). https://doi.org/10.1038/nprot.2009.81

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