Organism : Geobacter sulfurreducens | Module List :
GSU0267

transcriptional regulator, GntR family (VIMSS)

CircVis
Functional Annotations (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0267
(Mouseover regulator name to see its description)

GSU0267 is regulated by 21 influences and regulates 9 modules.
Regulators for GSU0267 (21)
Regulator Module Operator
GSU0267 206 tf
GSU0372 206 tf
GSU1250 206 tf
GSU2041 206 tf
GSU2202 206 tf
GSU2698 206 tf
GSU2831 206 tf
GSU2915 206 tf
GSU3387 206 tf
GSU0079 118 tf
GSU0266 118 tf
GSU0267 118 tf
GSU0372 118 tf
GSU0770 118 tf
GSU1727 118 tf
GSU1887 118 tf
GSU1989 118 tf
GSU2237 118 tf
GSU2262 118 tf
GSU2524 118 tf
GSU3387 118 tf

Warning: GSU0267 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
2396 5.00e+04 cCGGtCcGTgCaaGG
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2397 5.30e+04 TtGAAaTATAa
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2572 4.40e+01 AtTattTTaT
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2573 1.70e+03 AtTaaTCaTcAT
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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 GSU0267

GSU0267 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for GSU0267

GSU0267 has total of 50 gene neighbors in modules 118, 206
Gene neighbors (50)
Gene Common Name Description Module membership
GSU0030 GSU0030 oxygen-independent coproporphyrinogen III oxidase, putative (VIMSS) 118, 266
GSU0143 GSU0143 competence/damage-inducible protein CinA (VIMSS) 109, 118
GSU0163 GSU0163 hypothetical protein (VIMSS) 148, 206
GSU0168 GSU0168 Fic family protein (NCBI) 118, 319
GSU0204 GSU0204 radical SAM domain protein (NCBI) 118, 206
GSU0206 GSU0206 ZIP zinc transporter family protein (VIMSS) 189, 206
GSU0266 GSU0266 transcriptional regulator, LysR family (VIMSS) 118, 294
GSU0267 GSU0267 transcriptional regulator, GntR family (VIMSS) 118, 206
GSU0296 cheA chemotaxis protein CheA, putative (NCBI) 206, 266
GSU0315 GSU0315 hypothetical protein (VIMSS) 86, 206
GSU0355 GSU0355 hypothetical protein (VIMSS) 118, 319
GSU0518 GSU0518 sodium/solute symporter family protein (VIMSS) 118, 220
GSU0676 GSU0676 lipoprotein, putative (VIMSS) 118, 312
GSU0701 GSU0701 cytochrome c family protein (NCBI) 79, 206
GSU0770 GSU0770 transcriptional regulator, TetR family (VIMSS) 104, 118
GSU0915 GSU0915 hypothetical protein (VIMSS) 86, 206
GSU1041 GSU1041 methyl-accepting chemotaxis protein (VIMSS) 155, 206
GSU1044 GSU1044 MutT/nudix family protein (VIMSS) 118, 266
GSU1080 GSU1080 hypothetical protein (VIMSS) 112, 206
GSU1148 GSU1148 sensor histidine kinase (VIMSS) 110, 118
GSU1250 GSU1250 sigma-54 dependent DNA-binding response regulator (VIMSS) 46, 206
GSU1306 GSU1306 PHP domain protein (NCBI) 118, 188
GSU1309 GSU1309 hypothetical protein (VIMSS) 118, 166
GSU1330 GSU1330 metal ion efflux outer membrane protein family protein, putative (NCBI) 60, 206
GSU1339 GSU1339 hypothetical protein (NCBI) 206, 341
GSU1340 GSU1340 ABC transporter, permease protein (VIMSS) 206, 341
GSU1431 GSU1431 conserved hypothetical protein (VIMSS) 118, 229
GSU1661 GSU1661 hypothetical protein (VIMSS) 27, 118
GSU1663 GSU1663 phosphorylase family protein (VIMSS) 84, 118
GSU1664 GSU1664 conserved hypothetical protein (VIMSS) 110, 118
GSU1988 GSU1988 hypothetical protein (VIMSS) 96, 206
GSU2122 GSU2122 TraG family protein (VIMSS) 71, 206
GSU2191 GSU2191 aldehyde ferredoxin oxidoreductase, tungsten-containing (VIMSS) 71, 206
GSU2202 GSU2202 transcriptional regulator, LysR family (VIMSS) 86, 206
GSU2317 GSU2317 trkA domain protein (NCBI) 110, 118
GSU2318 mma4 cyclopropane-fatty-acyl-phospholipid synthase, putative (NCBI) 118, 220
GSU2326 GSU2326 outer membrane lipoprotein (VIMSS) 118, 226
GSU2331 GSU2331 conserved hypothetical protein (VIMSS) 118, 148
GSU2423 GSU2423 methyl-accepting chemotaxis protein, putative (VIMSS) 63, 206
GSU2460 GSU2460 ribonuclease BN, putative (VIMSS) 118, 266
GSU2497 GSU2497 lipoprotein, putative (VIMSS) 206, 341
GSU2498 GSU2498 lipoprotein, putative (VIMSS) 206, 341
GSU2698 GSU2698 transcriptional regulator, TetR family (VIMSS) 86, 206
GSU2734 GSU2734 hypothetical protein (VIMSS) 118, 206
GSU2769 GSU2769 metallo-beta-lactamase family protein (VIMSS) 71, 206
GSU2983 GSU2983 hypothetical protein (VIMSS) 86, 206
GSU3103 hemK modification methylase, HemK family (NCBI) 118, 294
GSU3409 GSU3409 hypothetical protein (VIMSS) 97, 206
GSU3410 GSU3410 hypothetical protein (VIMSS) 97, 206
GSU3460 GSU3460 glycosyl transferase, group 2 family protein (VIMSS) 118, 294
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 GSU0267
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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