Organism : Geobacter sulfurreducens | Module List :
GSU1320

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 GSU1320
(Mouseover regulator name to see its description)

GSU1320 is regulated by 17 influences and regulates 30 modules.
Regulators for GSU1320 (17)
Regulator Module Operator
GSU1320 14 tf
GSU1626 14 tf
GSU2581 14 tf
GSU2587 14 tf
GSU2716 14 tf
GSU2753 14 tf
GSU3217 14 tf
GSU0041 174 tf
GSU0187 174 tf
GSU1320 174 tf
GSU1495 174 tf
GSU1831 174 tf
GSU2809 174 tf
GSU2964 174 tf
GSU3041 174 tf
GSU3324 174 tf
GSU3370 174 tf

Warning: GSU1320 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
2188 9.80e+03 TattaTtataaTgtaTACatT
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2189 4.30e+02 GcGgTgcTcctGGTG.TgGcG
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2508 3.10e-07 aacacCTagaTTTACCTcatTtTC
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2509 5.30e-05 GgagcGCCagCcGcaaaAaGG
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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 GSU1320

GSU1320 is enriched for 9 functions in 3 categories.
Module neighborhood information for GSU1320

GSU1320 has total of 38 gene neighbors in modules 14, 174
Gene neighbors (38)
Gene Common Name Description Module membership
GSU0020 GSU0020 hexapeptide transferase family protein (VIMSS) 174, 332
GSU0121 GSU0121 nickel-iron hydrogenase, b-type cytochrome subunit (VIMSS) 14, 266
GSU0260 GSU0260 universal stress protein family (VIMSS) 14, 178
GSU0285 radA DNA repair protein RadA (NCBI) 15, 174
GSU0394 GSU0394 AcrB/AcrD/AcrF family protein (VIMSS) 14, 229
GSU0411 fliG flagellar motor switch protein FliG (NCBI) 14, 186
GSU0456 GSU0456 membrane protein, putative (VIMSS) 174, 221
GSU0558 GSU0558 hypothetical protein (VIMSS) 16, 174
GSU0571 folA dihydrofolate reductase (NCBI) 14, 281
GSU0659 GSU0659 polysaccharide deacetylase domain protein (VIMSS) 14, 97
GSU0880 GSU0880 molybdopterin oxidoreductase family protein (NCBI) 174, 306
GSU1031 GSU1031 hypothetical protein (VIMSS) 14, 337
GSU1064 GSU1064 hypothetical protein (VIMSS) 14, 220
GSU1076 ruvA Holliday junction DNA helicase RuvA (NCBI) 39, 174
GSU1154 GSU1154 surface repeat protein, putative (NCBI) 14, 268
GSU1204 GSU1204 sodium/hydrogen exchanger family/TrkA domain protein (VIMSS) 14, 282
GSU1210 GSU1210 metallo-beta-lactamase family protein (NCBI) 174, 196
GSU1300 GSU1300 methyl-accepting chemotaxis protein (VIMSS) 14, 78
GSU1320 GSU1320 sigma-54 dependent DNA-binding response regulator (VIMSS) 14, 174
GSU1371 GSU1371 oxidoreductase, FAD/FMN-binding (NCBI) 14, 107
GSU1482 GSU1482 outer membrane efflux protein (VIMSS) 14, 295
GSU1755 pyrD dihydroorotate dehydrogenase (NCBI) 143, 174
GSU1756 GSU1756 dihydroorotate dehydrogenase, electron transfer subunit, putative (NCBI) 174, 196
GSU1929 GSU1929 MgtC family protein (VIMSS) 174, 306
GSU1930 mglA1 GTP-binding domain protein (NCBI) 174, 332
GSU1933 fusA-1 translation elongation factor G (NCBI) 174, 196
GSU1948 GSU1948 hypothetical protein (VIMSS) 14, 292
GSU2138 GSU2138 hypothetical protein (VIMSS) 174, 318
GSU2169 GSU2169 hypothetical protein (VIMSS) 96, 174
GSU2365 rfbD dTDP-4-dehydrorhamnose reductase (NCBI) 174, 306
GSU2558 GSU2558 conserved domain protein (VIMSS) 39, 174
GSU2581 GSU2581 sigma-54 dependent transcriptional regulator (VIMSS) 14, 186
GSU2907 GSU2907 membrane protein, putative (VIMSS) 14, 109
GSU2928 GSU2928 hypothetical protein (VIMSS) 174, 282
GSU2959 GSU2959 membrane protein, putative (NCBI) 14, 213
GSU2981 GSU2981 TonB-dependent receptor, putative (VIMSS) 14, 148
GSU3081 GSU3081 conserved hypothetical protein, truncation (NCBI) 174, 201
GSU3419 GSU3419 sensor histidine kinase (VIMSS) 14, 274
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 GSU1320
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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