Organism : Geobacter sulfurreducens | Module List :
GSU3396

transcriptional regulator, GntR family (VIMSS)

CircVis
Functional Annotations (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU3396
(Mouseover regulator name to see its description)

GSU3396 is regulated by 15 influences and regulates 30 modules.
Regulators for GSU3396 (15)
Regulator Module Operator
GSU0164 295 tf
GSU1320 295 tf
GSU1483 295 tf
GSU1653 295 tf
GSU2753 295 tf
GSU2964 295 tf
GSU3396 295 tf
GSU0473 178 tf
GSU1410 178 tf
GSU1522 178 tf
GSU1626 178 tf
GSU1727 178 tf
GSU2926 178 tf
GSU3217 178 tf
GSU3229 178 tf

Warning: GSU3396 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
2516 3.20e+01 GTATcTTTaCtAAGtAaccgATA
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2517 5.60e+03 tgCaa.accG.t.AtTGAcA
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2748 1.20e+03 AaATctatTGATtcT
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2749 7.30e+03 TTTACATGaAaT.T
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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 GSU3396

GSU3396 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcriptional regulators cog/ cog
fatty-acyl-CoA binding go/ molecular_function
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
regulation of fatty acid metabolic process go/ biological_process
Module neighborhood information for GSU3396

GSU3396 has total of 48 gene neighbors in modules 178, 295
Gene neighbors (48)
Gene Common Name Description Module membership
GSU0010 GSU0010 sensory box histidine kinase/response regulator (VIMSS) 39, 295
GSU0202 GSU0202 conserved hypothetical protein (NCBI) 178, 339
GSU0249 GSU0249 membrane protein, putative (VIMSS) 55, 295
GSU0260 GSU0260 universal stress protein family (VIMSS) 14, 178
GSU0261 GSU0261 sodium/hydrogen exchanger family protein (VIMSS) 32, 178
GSU0387 GSU0387 undecaprenol kinase, putative (VIMSS) 89, 295
GSU0443 GSU0443 ribonuclease D, putative (VIMSS) 89, 295
GSU0450 GSU0450 conserved hypothetical protein (VIMSS) 178, 259
GSU0480 GSU0480 NifU-like domain protein (NCBI) 130, 178
GSU0573 GSU0573 alcohol dehydrogenase, zinc-containing (VIMSS) 295, 322
GSU0710 GSU0710 hypothetical protein (VIMSS) 178, 288
GSU0728 GSU0728 conserved hypothetical protein (VIMSS) 178, 261
GSU0745 GSU0745 NAD-dependent dehydrogenase subunit (NCBI) 178, 238
GSU0971 prfA peptidyl-tRNA hydrolase domain protein (NCBI) 153, 178
GSU0974 GSU0974 hypothetical protein (VIMSS) 178, 250
GSU1075 ruvC crossover junction endodeoxyribonuclease RuvC (NCBI) 233, 295
GSU1124 coaBC phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase (NCBI) 126, 295
GSU1172 mviN virulence factor mviN protein (NCBI) 295, 300
GSU1271 pyrB aspartate carbamoyltransferase (NCBI) 39, 295
GSU1292 GSU1292 sensory box histidine kinase (VIMSS) 35, 295
GSU1376 GSU1376 hypothetical protein (VIMSS) 178, 218
GSU1444 GSU1444 conserved hypothetical protein (VIMSS) 103, 295
GSU1460 proS prolyl-tRNA synthetase (NCBI) 233, 295
GSU1482 GSU1482 outer membrane efflux protein (VIMSS) 14, 295
GSU1653 GSU1653 sigma-54 dependent DNA-binding response regulator (VIMSS) 146, 295
GSU1702 GSU1702 ROK family protein (VIMSS) 204, 295
GSU2053 GSU2053 indolepyruvate ferredoxin oxidoreductase, alpha subunit, putative (VIMSS) 52, 295
GSU2092 GSU2092 conserved hypothetical protein (VIMSS) 142, 295
GSU2098 cooS carbon monoxide dehydrogenase subunit (NCBI) 1, 178
GSU2214 cheB-3 protein-glutamate methylesterase (NCBI) 126, 295
GSU2215 cheR-3 chemotaxis protein methyltransferase CheR (NCBI) 295, 323
GSU2231 GSU2231 conserved hypothetical protein (VIMSS) 262, 295
GSU2243 GSU2243 UDP-N-acetylglucosamine 2-epimerase (VIMSS) 295, 308
GSU2487 arcC carbamate kinase (NCBI) 178, 220
GSU2494 GSU2494 cytochrome c family protein (VIMSS) 46, 178
GSU2595 GSU2595 hypothetical protein (VIMSS) 27, 295
GSU2596 GSU2596 lipoprotein, putative (VIMSS) 179, 295
GSU2609 pilB type IV pilus assembly protein, putative (NCBI) 227, 295
GSU2914 GSU2914 NHL repeat protein (NCBI) 178, 259
GSU2948 GSU2948 membrane protein, putative (NCBI) 103, 178
GSU3008 cobS cobalamin 5'-phosphate synthase (NCBI) 30, 295
GSU3017 GSU3017 conserved domain protein (VIMSS) 178, 244
GSU3189 GSU3189 hypothetical protein (VIMSS) 178, 252
GSU3264 GSU3264 membrane protein, putative (VIMSS) 295, 300
GSU3265 nirB sulfite reductase, assimilatory-type (NCBI) 295, 327
GSU3346 GSU3346 potassium uptake protein, Kup system (VIMSS) 249, 295
GSU3395 putA proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase (NCBI) 178, 294
GSU3396 GSU3396 transcriptional regulator, GntR family (VIMSS) 178, 295
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 GSU3396
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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