Organism : Geobacter sulfurreducens | Module List :
GSU3217

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 GSU3217
(Mouseover regulator name to see its description)

GSU3217 is regulated by 21 influences and regulates 34 modules.
Regulators for GSU3217 (21)
Regulator Module Operator
GSU0266 92 tf
GSU0770 92 tf
GSU1626 92 tf
GSU1989 92 tf
GSU2524 92 tf
GSU2915 92 tf
GSU3108 92 tf
GSU3217 92 tf
GSU3387 92 tf
GSU0063 287 tf
GSU0735 287 tf
GSU0812 287 tf
GSU2041 287 tf
GSU2581 287 tf
GSU2587 287 tf
GSU2716 287 tf
GSU2779 287 tf
GSU2787 287 tf
GSU2868 287 tf
GSU3217 287 tf
GSU3363 287 tf

Warning: GSU3217 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
2344 2.10e+03 gTgtTAaCG.Aagcg.aAa...G
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2345 2.10e+04 GGcaTCaCcGCTgTC
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2732 1.00e+01 gTAAAAat.aCCCacT
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2733 1.10e+03 tT.TTCcTCTagccTAacCaacCt
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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 GSU3217

GSU3217 is enriched for 9 functions in 3 categories.
Module neighborhood information for GSU3217

GSU3217 has total of 44 gene neighbors in modules 92, 287
Gene neighbors (44)
Gene Common Name Description Module membership
GSU0046 GSU0046 ISGsu6, transposase OrfA (VIMSS) 92, 211
GSU0048 GSU0048 integrase (NCBI) 287, 300
GSU0252 GSU0252 ISGsu1, transposase (VIMSS) 92, 211
GSU0270 glmS glucosamine--fructose-6-phosphate aminotransferase (isomerizing) (NCBI) 285, 287
GSU0286 GSU0286 PBS lyase HEAT-like repeat protein (NCBI) 92, 107
GSU0398 GSU0398 phage shock protein E, putative (VIMSS) 92, 163
GSU0424 fliQ flagellar biosynthetic protein FliQ (NCBI) 92, 217
GSU0547 mutS2 MutS2 family protein (NCBI) 252, 287
GSU0549 GSU0549 conserved domain protein (NCBI) 122, 287
GSU0582 GSU0582 methyl-accepting chemotaxis protein (VIMSS) 281, 287
GSU0605 thiD thiamine-phosphate pyrophosphorylase/phosphomethylpyrimidine kinase (NCBI) 99, 287
GSU0828 GSU0828 metal ion efflux outer membrane protein family protein, putative (VIMSS) 27, 92
GSU0901 fragment conserved domain protein (NCBI) 257, 287
GSU0916 GSU0916 methyl-accepting chemotaxis protein (VIMSS) 186, 287
GSU0955 GSU0955 group II intron, maturase (VIMSS) 92, 211
GSU0961 GSU0961 ISGsu4, transposase (VIMSS) 92, 211
GSU1020 GSU1020 hypothetical protein (VIMSS) 92, 132
GSU1029 GSU1029 methyl-accepting chemotaxis protein (VIMSS) 63, 287
GSU1034 GSU1034 None 287, 300
GSU1101 GSU1101 sensory box histidine kinase (VIMSS) 252, 287
GSU1383 dnaQ exonuclease (NCBI) 287, 300
GSU1400 GSU1400 None 38, 92
GSU1552 GSU1552 conserved hypothetical protein (VIMSS) 220, 287
GSU1567 htpX peptidase, M48 family (NCBI) 78, 287
GSU1742 GSU1742 Na/Pi-cotransporter family protein (VIMSS) 287, 293
GSU1767 xseA exodeoxyribonuclease VII, large subunit (NCBI) 92, 218
GSU2094 GSU2094 response regulator (VIMSS) 1, 287
GSU2300 GSU2300 hypothetical protein (VIMSS) 99, 287
GSU2320 GSU2320 hypothetical protein (VIMSS) 92, 294
GSU2343 GSU2343 None 92, 132
GSU2346 GSU2346 membrane protein, putative (VIMSS) 92, 107
GSU2441 GSU2441 conserved hypothetical protein (VIMSS) 287, 317
GSU2500 GSU2500 hypothetical protein (NCBI) 92, 213
GSU2574 GSU2574 response regulator (VIMSS) 122, 287
GSU2594 GSU2594 ISGsu6, transposase OrfB (VIMSS) 287, 300
GSU2659 GSU2659 hypothetical protein (VIMSS) 183, 287
GSU2661 GSU2661 conserved hypothetical protein (VIMSS) 1, 287
GSU2759 GSU2759 potassium efflux system protein (VIMSS) 183, 287
GSU2984 znuC permease component of zinc ABC transporter (Dmitry Rodionov) 96, 287
GSU3150 GSU3150 HPP family protein (NCBI) 26, 287
GSU3217 GSU3217 sigma-54 dependent DNA-binding response regulator (VIMSS) 92, 287
GSU3224 GSU3224 hypothetical protein (VIMSS) 287, 337
GSU3372 GSU3372 cardiolipin synthetase, putative (VIMSS) 287, 291
GSU3387 GSU3387 transcriptional regulator, AraC/XylS family (VIMSS) 92, 283
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 GSU3217
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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