Organism : Geobacter sulfurreducens | Module List :
GSU3031

sigma-54 dependent transcriptional regulator (VIMSS)

CircVis
Functional Annotations (6)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3031
(Mouseover regulator name to see its description)

GSU3031 is regulated by 18 influences and regulates 0 modules.
Regulators for GSU3031 (18)
Regulator Module Operator
GSU1495 278 tf
GSU1569 278 tf
GSU2177 278 tf
GSU2202 278 tf
GSU2523 278 tf
GSU2915 278 tf
GSU0013 69 tf
GSU0359 69 tf
GSU0372 69 tf
GSU0551 69 tf
GSU0736 69 tf
GSU1039 69 tf
GSU2113 69 tf
GSU2177 69 tf
GSU2506 69 tf
GSU2523 69 tf
GSU3045 69 tf
GSU3053 69 tf

Warning: GSU3031 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
2298 3.00e+02 CTGtcTGaTcA
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2299 8.30e+03 catccaTtttCcCcTCCTta
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2716 1.10e+03 aCAggAAagGAgAA
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2717 5.30e+03 TTAAC.TTAaTttTaaT
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Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for GSU3031

GSU3031 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
Module neighborhood information for GSU3031

GSU3031 has total of 41 gene neighbors in modules 69, 278
Gene neighbors (41)
Gene Common Name Description Module membership
GSU0056 GSU0056 conserved hypothetical protein (VIMSS) 36, 69
GSU0273 GSU0273 radical SAM domain protein (NCBI) 249, 278
GSU0295 cheR-1 chemotaxis protein methyltransferase CheR (NCBI) 278, 338
GSU0314 GSU0314 general secretion protein E N-terminal domain protein (NCBI) 79, 278
GSU0397 GSU0397 Metallo-beta-lactamase family protein (VIMSS) 61, 69
GSU0413 fliI flagellum-specific ATP synthase FliI (NCBI) 186, 278
GSU0427 GSU0427 lipoprotein, putative (VIMSS) 96, 278
GSU0428 GSU0428 lipoprotein, putative (VIMSS) 21, 278
GSU0432 GSU0432 conserved hypothetical protein (VIMSS) 96, 278
GSU0512 GSU0512 conserved hypothetical protein (VIMSS) 8, 278
GSU0515 GSU0515 universal stress protein family (VIMSS) 69, 181
GSU0546 GSU0546 peptidyl-tRNA hydrolase domain protein (NCBI) 69, 252
GSU0705 GSU0705 cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) 36, 278
GSU0758 GSU0758 membrane protein, putative (VIMSS) 181, 278
GSU0759 GSU0759 hypothetical protein (VIMSS) 260, 278
GSU0833 GSU0833 hypothetical protein (VIMSS) 180, 278
GSU0899 GSU0899 conserved hypothetical protein (VIMSS) 69, 304
GSU1042 GSU1042 conserved hypothetical protein (NCBI) 130, 278
GSU1156 asnS asparaginyl-tRNA synthetase (NCBI) 104, 278
GSU1164 GSU1164 ABC transporter, permease protein (VIMSS) 130, 278
GSU1281 nikO component of nickel ABC transport system (Dmitry Rodionov) 181, 278
GSU1378 pbpE beta-lactamase (NCBI) 69, 201
GSU1391 GSU1391 Fic family protein (NCBI) 249, 278
GSU1611 GSU1611 AcrB/AcrD/AcrF family protein (VIMSS) 278, 338
GSU1740 GSU1740 cytochrome c family protein, putative (VIMSS) 69, 181
GSU1991 GSU1991 CAAX amino terminal protease family protein (NCBI) 222, 278
GSU2114 GSU2114 hypothetical protein (VIMSS) 278, 338
GSU2117 GSU2117 hypothetical protein (VIMSS) 181, 278
GSU2123 GSU2123 HD domain protein (NCBI) 104, 278
GSU2163 GSU2163 hypothetical protein (VIMSS) 181, 278
GSU2274 fbP-2 FKBP-type peptidyl-prolyl cis-trans isomerase (NCBI) 15, 278
GSU2295 GSU2295 hypothetical protein (VIMSS) 141, 278
GSU2385 GSU2385 hypothetical protein (VIMSS) 82, 278
GSU2402 GSU2402 hypothetical protein (VIMSS) 84, 278
GSU2533 GSU2533 hypothetical protein (VIMSS) 224, 278
GSU2782 GSU2782 AcrB/AcrD/AcrF family protein (VIMSS) 278, 296
GSU3031 GSU3031 sigma-54 dependent transcriptional regulator (VIMSS) 69, 278
GSU3118 regX3 DNA-binding response regulator (NCBI) 253, 278
GSU3119 GSU3119 sensor histidine kinase (VIMSS) 180, 278
GSU3261 GSU3261 response regulator (VIMSS) 69, 307
GSU3262 uvrB excinuclease ABC, B subunit (NCBI) 61, 69
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for GSU3031
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend