Organism : Geobacter sulfurreducens | Module List :
GSU2670

transcriptional regulator, LuxR family (VIMSS)

CircVis
Functional Annotations (5)
Function System
DNA-binding HTH domain-containing proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2670
(Mouseover regulator name to see its description)

GSU2670 is regulated by 18 influences and regulates 24 modules.
Regulators for GSU2670 (18)
Regulator Module Operator
GSU0280 303 tf
GSU0776 303 tf
GSU1250 303 tf
GSU1268 303 tf
GSU1653 303 tf
GSU2506 303 tf
GSU2670 303 tf
GSU0280 105 tf
GSU0598 105 tf
GSU0721 105 tf
GSU1268 105 tf
GSU1653 105 tf
GSU2506 105 tf
GSU2670 105 tf
GSU2753 105 tf
GSU2779 105 tf
GSU3396 105 tf
GSU3457 105 tf

Warning: GSU2670 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
2370 1.80e+02 TatTGcggaTgtcaatatt.A.ta
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2371 1.40e+04 cT.TTccAaTt
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2764 1.50e+01 TaGAAcTTAaaTTaAaaaTTCTG
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2765 1.70e+01 ACCctcatCGaaAATaTGtCG
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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 GSU2670

GSU2670 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
DNA-binding HTH domain-containing proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for GSU2670

GSU2670 has total of 45 gene neighbors in modules 105, 303
Gene neighbors (45)
Gene Common Name Description Module membership
GSU0495 GSU0495 hypothetical protein (VIMSS) 57, 303
GSU0956 GSU0956 hypothetical protein (VIMSS) 105, 148
GSU1264 GSU1264 conserved domain protein (VIMSS) 103, 105
GSU1265 GSU1265 sensor histidine kinase/response regulator (VIMSS) 103, 105
GSU1385 GSU1385 conserved hypothetical protein (VIMSS) 36, 105
GSU1387 GSU1387 CRISPR-associated protein, CT1975 family (NCBI) 105, 303
GSU1389 GSU1389 CRISPR-associated protein, CT1974 family (NCBI) 105, 303
GSU1442 GSU1442 carbonic anhydrase family protein (VIMSS) 117, 303
GSU1455 GSU1455 hypothetical protein (VIMSS) 105, 330
GSU1471 GSU1471 HD domain protein (VIMSS) 124, 303
GSU1472 GSU1472 hypothetical protein (VIMSS) 124, 303
GSU1473 GSU1473 membrane protein, putative (VIMSS) 124, 303
GSU1474 GSU1474 DedA family protein (NCBI) 124, 303
GSU1476 GSU1476 hypothetical protein (VIMSS) 105, 124
GSU1498 GSU1498 membrane protein, putative (VIMSS) 254, 303
GSU1499 GSU1499 membrane protein, putative (VIMSS) 105, 303
GSU1500 GSU1500 hypothetical protein (VIMSS) 103, 105
GSU1501 GSU1501 ABC transporter, ATP-binding protein (VIMSS) 103, 303
GSU1502 GSU1502 prenyltransferase, UbiA family (VIMSS) 103, 105
GSU1504 GSU1504 ABC transporter, permease protein, ABC-2 family (VIMSS) 103, 105
GSU1505 GSU1505 ABC transporter, ATP-binding protein (VIMSS) 103, 105
GSU1506 GSU1506 hypothetical protein (VIMSS) 254, 303
GSU1507 GSU1507 heptosyltransferase family protein, putative (VIMSS) 105, 158
GSU1510 GSU1510 glycosyl transferase, group 2 family protein (VIMSS) 105, 179
GSU1544 GSU1544 hypothetical protein (VIMSS) 8, 105
GSU1954 GSU1954 membrane protein, putative (VIMSS) 105, 247
GSU1955 GSU1955 capK related-protein (NCBI) 105, 247
GSU2058 GSU2058 hypothetical protein (VIMSS) 34, 303
GSU2074 GSU2074 PPIC-type PPIASE domain protein (NCBI) 48, 303
GSU2172 GSU2172 OmpA domain protein, putative (VIMSS) 105, 191
GSU2397 GSU2397 conserved hypothetical protein (VIMSS) 105, 254
GSU2467 GSU2467 hypothetical protein/integrase, fusion (VIMSS) 303, 324
GSU2468 GSU2468 hypothetical protein (VIMSS) 303, 324
GSU2470 GSU2470 hypothetical protein (VIMSS) 254, 303
GSU2670 GSU2670 transcriptional regulator, LuxR family (VIMSS) 105, 303
GSU2943 GSU2943 hypothetical protein (VIMSS) 103, 105
GSU3170 GSU3170 hypothetical protein (VIMSS) 103, 303
GSU3172 GSU3172 conserved hypothetical protein (VIMSS) 103, 303
GSU3174 hcP-2 hcp protein (NCBI) 117, 303
GSU3175 GSU3175 hypothetical protein (VIMSS) 103, 303
GSU3176 GSU3176 lysM domain protein (NCBI) 105, 303
GSU3177 GSU3177 Rhs family protein (NCBI) 103, 105
GSU3178 GSU3178 hypothetical protein (VIMSS) 105, 146
GSU3179 GSU3179 conserved domain protein (NCBI) 105, 130
GSU3185 GSU3185 hypothetical protein (VIMSS) 103, 105
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 GSU2670
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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