Limits...
From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet.

Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J - Nucleic Acids Res. (2009)

Bottom Line: We designed a bioinformatics pipeline for the reliable transfer of gene regulations between taxonomically closely related organisms that incorporates (i) a prediction of orthologous genes and (ii) the prediction of transcription factor binding sites.Based on that, we designed a publicly available platform that aims to data integration, analysis, visualization and finally the reconstruction of mycobacterial transcriptional gene regulatory networks: MycoRegNet.It is a comprehensive database system and analysis platform that offers several methods for data exploration and the generation of novel hypotheses.

View Article: PubMed Central - PubMed

Affiliation: Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany and International Computer Science Institute, Berkeley, CA, USA.

ABSTRACT
Year by year, approximately two million people die from tuberculosis, a disease caused by the bacterium Mycobacterium tuberculosis. There is a tremendous need for new anti-tuberculosis therapies (antituberculotica) and drugs to cope with the spread of tuberculosis. Despite many efforts to obtain a better understanding of M. tuberculosis' pathogenicity and its survival strategy in humans, many questions are still unresolved. Among other cellular processes in bacteria, pathogenicity is controlled by transcriptional regulation. Thus, various studies on M. tuberculosis concentrate on the analysis of transcriptional regulation in order to gain new insights on pathogenicity and other essential processes ensuring mycobacterial survival. We designed a bioinformatics pipeline for the reliable transfer of gene regulations between taxonomically closely related organisms that incorporates (i) a prediction of orthologous genes and (ii) the prediction of transcription factor binding sites. In total, 460 regulatory interactions were identified for M. tuberculosis using our comparative approach. Based on that, we designed a publicly available platform that aims to data integration, analysis, visualization and finally the reconstruction of mycobacterial transcriptional gene regulatory networks: MycoRegNet. It is a comprehensive database system and analysis platform that offers several methods for data exploration and the generation of novel hypotheses. MycoRegNet is publicly available at http://mycoregnet.cebitec.uni-bielefeld.de.

Show MeSH

Related in: MedlinePlus

MycoRegNet main page. The main page includes a typical search mask, a statistical overview of the database content, an entry point to browse the integrated organisms, and links to more specific statistics, the system documentation and a tutorial on how to use the MycoRegNet Web Service.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2724278&req=5

Figure 2: MycoRegNet main page. The main page includes a typical search mask, a statistical overview of the database content, an entry point to browse the integrated organisms, and links to more specific statistics, the system documentation and a tutorial on how to use the MycoRegNet Web Service.

Mentions: As for other online databases, MycoRegNet's web interface provides the three major capabilities: browsing the database content, searching by specifying filter criteria and basic visualization possibilities. Furthermore, the front-end offers the execution of computational features. At the main page (Figure 2), one has the option to search or to browse the database content. The user may browse the data repository by clicking on an ecotype name of interest and is provided with an overview on the selected organism. Alternatively, using one of the provided options within the search form, the database can be searched for specific gene/protein identifiers, gene/protein names, regulator types or functional modules. The search results are presented in tabular form, listing all relevant information for subsequent investigation. Furthermore, the following built-in features can be accessed from the main page, directly: TFBScan [for TFBS predictions; see below) and COMA (to check for contradictions within microarray gene expression studies, given the regulatory network stored in the database; refer to (8) for more details]. Detailed information on the results can be obtained via respective links at the result page. By selecting a particular gene, the corresponding gene details page is invoked. It presents a detailed overview of all available data attached to the gene of interest. Besides general information about the gene/protein (position in the genome, nucleotide sequence, etc.), it comprises a graphical representation of the genomic context, regulated target genes (if encoding a TF) including the TFBSs, etc., and stimulons that initiate a differential gene expression level. The integrated Web Service client for GenDB maintains the representation of up-to-date gene annotation data. General information (description, comments, an assigned function, etc.) is listed as well as the EC numbers for enzymes, and links to COG (41) and GO (42). Additionally, all target genes of a TF of interest, are linked to KEGG pathways and a list of regulated pathways is displayed.Figure 2.


From Corynebacterium glutamicum to Mycobacterium tuberculosis--towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet.

Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J - Nucleic Acids Res. (2009)

MycoRegNet main page. The main page includes a typical search mask, a statistical overview of the database content, an entry point to browse the integrated organisms, and links to more specific statistics, the system documentation and a tutorial on how to use the MycoRegNet Web Service.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2724278&req=5

Figure 2: MycoRegNet main page. The main page includes a typical search mask, a statistical overview of the database content, an entry point to browse the integrated organisms, and links to more specific statistics, the system documentation and a tutorial on how to use the MycoRegNet Web Service.
Mentions: As for other online databases, MycoRegNet's web interface provides the three major capabilities: browsing the database content, searching by specifying filter criteria and basic visualization possibilities. Furthermore, the front-end offers the execution of computational features. At the main page (Figure 2), one has the option to search or to browse the database content. The user may browse the data repository by clicking on an ecotype name of interest and is provided with an overview on the selected organism. Alternatively, using one of the provided options within the search form, the database can be searched for specific gene/protein identifiers, gene/protein names, regulator types or functional modules. The search results are presented in tabular form, listing all relevant information for subsequent investigation. Furthermore, the following built-in features can be accessed from the main page, directly: TFBScan [for TFBS predictions; see below) and COMA (to check for contradictions within microarray gene expression studies, given the regulatory network stored in the database; refer to (8) for more details]. Detailed information on the results can be obtained via respective links at the result page. By selecting a particular gene, the corresponding gene details page is invoked. It presents a detailed overview of all available data attached to the gene of interest. Besides general information about the gene/protein (position in the genome, nucleotide sequence, etc.), it comprises a graphical representation of the genomic context, regulated target genes (if encoding a TF) including the TFBSs, etc., and stimulons that initiate a differential gene expression level. The integrated Web Service client for GenDB maintains the representation of up-to-date gene annotation data. General information (description, comments, an assigned function, etc.) is listed as well as the EC numbers for enzymes, and links to COG (41) and GO (42). Additionally, all target genes of a TF of interest, are linked to KEGG pathways and a list of regulated pathways is displayed.Figure 2.

Bottom Line: We designed a bioinformatics pipeline for the reliable transfer of gene regulations between taxonomically closely related organisms that incorporates (i) a prediction of orthologous genes and (ii) the prediction of transcription factor binding sites.Based on that, we designed a publicly available platform that aims to data integration, analysis, visualization and finally the reconstruction of mycobacterial transcriptional gene regulatory networks: MycoRegNet.It is a comprehensive database system and analysis platform that offers several methods for data exploration and the generation of novel hypotheses.

View Article: PubMed Central - PubMed

Affiliation: Computational Genomics, Center for Biotechnology, Bielefeld University, Bielefeld, Germany and International Computer Science Institute, Berkeley, CA, USA.

ABSTRACT
Year by year, approximately two million people die from tuberculosis, a disease caused by the bacterium Mycobacterium tuberculosis. There is a tremendous need for new anti-tuberculosis therapies (antituberculotica) and drugs to cope with the spread of tuberculosis. Despite many efforts to obtain a better understanding of M. tuberculosis' pathogenicity and its survival strategy in humans, many questions are still unresolved. Among other cellular processes in bacteria, pathogenicity is controlled by transcriptional regulation. Thus, various studies on M. tuberculosis concentrate on the analysis of transcriptional regulation in order to gain new insights on pathogenicity and other essential processes ensuring mycobacterial survival. We designed a bioinformatics pipeline for the reliable transfer of gene regulations between taxonomically closely related organisms that incorporates (i) a prediction of orthologous genes and (ii) the prediction of transcription factor binding sites. In total, 460 regulatory interactions were identified for M. tuberculosis using our comparative approach. Based on that, we designed a publicly available platform that aims to data integration, analysis, visualization and finally the reconstruction of mycobacterial transcriptional gene regulatory networks: MycoRegNet. It is a comprehensive database system and analysis platform that offers several methods for data exploration and the generation of novel hypotheses. MycoRegNet is publicly available at http://mycoregnet.cebitec.uni-bielefeld.de.

Show MeSH
Related in: MedlinePlus