Organism : Geobacter sulfurreducens | Module List :
GSU1250

sigma-54 dependent DNA-binding response regulator (VIMSS)

CircVis
Functional Annotations (9)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
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 GSU1250
(Mouseover regulator name to see its description)

GSU1250 is regulated by 19 influences and regulates 30 modules.
Regulators for GSU1250 (19)
Regulator Module Operator
GSU0267 206 tf
GSU0372 206 tf
GSU1250 206 tf
GSU2041 206 tf
GSU2202 206 tf
GSU2698 206 tf
GSU2831 206 tf
GSU2915 206 tf
GSU3387 206 tf
GSU0164 46 tf
GSU0655 46 tf
GSU1250 46 tf
GSU1268 46 tf
GSU1934 46 tf
GSU2262 46 tf
GSU2523 46 tf
GSU2670 46 tf
GSU2741 46 tf
GSU2771 46 tf

Warning: GSU1250 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
2252 1.30e+00 AtAAcC.GCACAaAACa
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2253 1.40e+02 aGtTcTAcAGTctGaaTAaa
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2572 4.40e+01 AtTattTTaT
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2573 1.70e+03 AtTaaTCaTcAT
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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 GSU1250

GSU1250 is enriched for 9 functions in 3 categories.
Module neighborhood information for GSU1250

GSU1250 has total of 51 gene neighbors in modules 46, 206
Gene neighbors (51)
Gene Common Name Description Module membership
GSU0163 GSU0163 hypothetical protein (VIMSS) 148, 206
GSU0182 GSU0182 lipoprotein, putative (VIMSS) 46, 292
GSU0183 GSU0183 lipoprotein, putative (VIMSS) 46, 325
GSU0204 GSU0204 radical SAM domain protein (NCBI) 118, 206
GSU0206 GSU0206 ZIP zinc transporter family protein (VIMSS) 189, 206
GSU0210 GSU0210 conserved hypothetical protein (VIMSS) 46, 91
GSU0211 GSU0211 ABC transporter, permease protein, putative (VIMSS) 46, 321
GSU0267 GSU0267 transcriptional regulator, GntR family (VIMSS) 118, 206
GSU0296 cheA chemotaxis protein CheA, putative (NCBI) 206, 266
GSU0315 GSU0315 hypothetical protein (VIMSS) 86, 206
GSU0492 xerD site-specific recombinase, phage integrase family (NCBI) 46, 49
GSU0701 GSU0701 cytochrome c family protein (NCBI) 79, 206
GSU0844 GSU0844 potassium uptake protein, Trk family (VIMSS) 46, 97
GSU0862 folD-2 folD bifunctional protein (NCBI) 46, 126
GSU0874 GSU0874 hypothetical protein (VIMSS) 46, 321
GSU0915 GSU0915 hypothetical protein (VIMSS) 86, 206
GSU1041 GSU1041 methyl-accepting chemotaxis protein (VIMSS) 155, 206
GSU1080 GSU1080 hypothetical protein (VIMSS) 112, 206
GSU1190 GSU1190 conserved hypothetical protein (VIMSS) 46, 253
GSU1250 GSU1250 sigma-54 dependent DNA-binding response regulator (VIMSS) 46, 206
GSU1330 GSU1330 metal ion efflux outer membrane protein family protein, putative (NCBI) 60, 206
GSU1332 GSU1332 heavy metal efflux pump, CzcA family (VIMSS) 46, 341
GSU1339 GSU1339 hypothetical protein (NCBI) 206, 341
GSU1340 GSU1340 ABC transporter, permease protein (VIMSS) 206, 341
GSU1403 rluB ribosomal large subunit pseudouridine synthase B (NCBI) 46, 201
GSU1837 GSU1837 peptidase, family M23/M37 domain protein (NCBI) 20, 46
GSU1875 ahcY adenosylhomocysteinase (NCBI) 20, 46
GSU1988 GSU1988 hypothetical protein (VIMSS) 96, 206
GSU2122 GSU2122 TraG family protein (VIMSS) 71, 206
GSU2150 GSU2150 hypothetical protein (VIMSS) 46, 142
GSU2191 GSU2191 aldehyde ferredoxin oxidoreductase, tungsten-containing (VIMSS) 71, 206
GSU2202 GSU2202 transcriptional regulator, LysR family (VIMSS) 86, 206
GSU2287 GSU2287 response regulator (VIMSS) 11, 46
GSU2288 GSU2288 sensor histidine kinase (VIMSS) 46, 77
GSU2289 GSU2289 nicotinate phosphoribosyltransferase, putative (NCBI) 46, 79
GSU2290 pncA pyrazinamidase/nicotinamidase, putative (NCBI) 46, 321
GSU2423 GSU2423 methyl-accepting chemotaxis protein, putative (VIMSS) 63, 206
GSU2476 GSU2476 TPR domain protein (VIMSS) 46, 220
GSU2494 GSU2494 cytochrome c family protein (VIMSS) 46, 178
GSU2497 GSU2497 lipoprotein, putative (VIMSS) 206, 341
GSU2498 GSU2498 lipoprotein, putative (VIMSS) 206, 341
GSU2529 fusA-2 translation elongation factor G (NCBI) 9, 46
GSU2698 GSU2698 transcriptional regulator, TetR family (VIMSS) 86, 206
GSU2734 GSU2734 hypothetical protein (VIMSS) 118, 206
GSU2769 GSU2769 metallo-beta-lactamase family protein (VIMSS) 71, 206
GSU2883 GSU2883 cytochrome c family protein (VIMSS) 20, 46
GSU2975 GSU2975 inorganic pyrophosphatase, manganese-dependent, putative (VIMSS) 46, 220
GSU2983 GSU2983 hypothetical protein (VIMSS) 86, 206
GSU3348 hslO chaperonin, 33 kDa family (NCBI) 46, 321
GSU3409 GSU3409 hypothetical protein (VIMSS) 97, 206
GSU3410 GSU3410 hypothetical protein (VIMSS) 97, 206
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 GSU1250
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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