Organism : Geobacter sulfurreducens | Module List :
GSU0254

DNA-binding response regulator, LuxR family (VIMSS)

CircVis
Functional Annotations (10)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain 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
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
protein-glutamate methylesterase activity go/ molecular_function
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0254
(Mouseover regulator name to see its description)

GSU0254 is regulated by 21 influences and regulates 19 modules.
Regulators for GSU0254 (21)
Regulator Module Operator
GSU0013 107 tf
GSU0107 107 tf
GSU0254 107 tf
GSU0473 107 tf
GSU0655 107 tf
GSU0896 107 tf
GSU1095 107 tf
GSU1268 107 tf
GSU1410 107 tf
GSU1626 107 tf
GSU2523 107 tf
GSU2587 107 tf
GSU0178 77 tf
GSU0776 77 tf
GSU1342 77 tf
GSU1345 77 tf
GSU1653 77 tf
GSU1940 77 tf
GSU2033 77 tf
GSU2354 77 tf
GSU3324 77 tf

Warning: GSU0254 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
2314 1.30e+04 TAta.tA.tgAaTgGtaTttTTC
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2315 1.00e+04 cCATttTaT..agAC
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2374 2.30e+03 atCtCAgctaaatCaataaA
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2375 3.10e+03 AtTcCGGgTgCtG.tcgctcGt.A
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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 GSU0254

GSU0254 is enriched for 10 functions in 3 categories.
Module neighborhood information for GSU0254

GSU0254 has total of 45 gene neighbors in modules 77, 107
Gene neighbors (45)
Gene Common Name Description Module membership
GSU0126 GSU0126 iron-sulfur cluster-binding protein (VIMSS) 107, 218
GSU0150 argB acetylglutamate kinase (NCBI) 107, 189
GSU0151 argD acetylornithine aminotransferase (NCBI) 107, 336
GSU0253 GSU0253 sensory box histidine kinase (VIMSS) 4, 107
GSU0254 GSU0254 DNA-binding response regulator, LuxR family (VIMSS) 77, 107
GSU0286 GSU0286 PBS lyase HEAT-like repeat protein (NCBI) 92, 107
GSU0356 GSU0356 None 96, 107
GSU0363 dinG ATP-dependent helicase DinG (NCBI) 107, 266
GSU0439 GSU0439 4-hydroxybenzoate octaprenyltransferase, putative (VIMSS) 107, 317
GSU0473 GSU0473 transcriptional regulator, putative (VIMSS) 107, 132
GSU0476 GSU0476 conserved hypothetical protein (VIMSS) 77, 264
GSU0499 GSU0499 M23/M37 peptidase domain protein (VIMSS) 77, 94
GSU0503 crcB crcB protein (NCBI) 77, 121
GSU0642 ffh signal recognition particle protein (NCBI) 107, 200
GSU0646 trmD tRNA (guanine-N1)-methyltransferase (NCBI) 107, 200
GSU0686 dxs-1 deoxyxylulose-5-phosphate synthase (NCBI) 107, 309
GSU0687 GSU0687 dihydroflavonol 4-reductase, putative (NCBI) 107, 309
GSU0688 shc-1 squalene-hopene cyclase (NCBI) 107, 309
GSU0791 GSU0791 conserved hypothetical protein (VIMSS) 107, 252
GSU1017 hpt hypoxanthine phosphoribosyltransferase, putative (NCBI) 20, 77
GSU1082 GSU1082 conserved hypothetical protein (VIMSS) 16, 77
GSU1125 GSU1125 hypothetical protein (VIMSS) 77, 203
GSU1261 GSU1261 ABC transporter, ATP-binding protein (VIMSS) 77, 176
GSU1290 cheA-1 chemotaxis protein CheA (NCBI) 55, 77
GSU1371 GSU1371 oxidoreductase, FAD/FMN-binding (NCBI) 14, 107
GSU1666 GSU1666 iron-sulfur cluster-binding protein (NCBI) 77, 124
GSU1966 GSU1966 conserved hypothetical protein (VIMSS) 77, 90
GSU2040 GSU2040 hypothetical protein (VIMSS) 107, 132
GSU2112 GSU2112 hypothetical protein (VIMSS) 68, 77
GSU2207 GSU2207 DNA polymerase III, delta subunit, putative (NCBI) 77, 94
GSU2208 GSU2208 lipoprotein, putative (VIMSS) 77, 94
GSU2209 leuS leucyl-tRNA synthetase (NCBI) 15, 77
GSU2217 GSU2217 response regulator (VIMSS) 77, 94
GSU2288 GSU2288 sensor histidine kinase (VIMSS) 46, 77
GSU2328 GSU2328 None 107, 132
GSU2346 GSU2346 membrane protein, putative (VIMSS) 92, 107
GSU2623 GSU2623 peptide ABC transporter, ATP-binding protein (VIMSS) 77, 152
GSU2685 GSU2685 membrane protein, putative (VIMSS) 99, 107
GSU2767 GSU2767 cytochrome c family protein, putative (NCBI) 107, 266
GSU2933 GSU2933 cytochrome b/b6 complex, iron-sulfur subunit (VIMSS) 107, 266
GSU3135 lspA lipoprotein signal peptidase (NCBI) 77, 238
GSU3187 GSU3187 ferredoxin family protein (VIMSS) 77, 124
GSU3244 GSU3244 hypothetical protein (VIMSS) 73, 77
GSU3269 GSU3269 None 38, 107
GSU3456 def-2 polypeptide deformylase (NCBI) 107, 336
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 GSU0254
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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