Organism : Geobacter sulfurreducens | Module List :
GSU0951

transcriptional regulator, TetR family (VIMSS)

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0951
(Mouseover regulator name to see its description)

GSU0951 is regulated by 13 influences and regulates 8 modules.
Regulators for GSU0951 (13)
Regulator Module Operator
GSU0300 82 tf
GSU0951 82 tf
GSU1863 82 tf
GSU1940 82 tf
GSU2354 82 tf
GSU2506 82 tf
GSU3053 82 tf
GSU1320 296 tf
GSU1639 296 tf
GSU2787 296 tf
GSU2809 296 tf
GSU2915 296 tf
GSU3053 296 tf

Warning: GSU0951 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
2324 1.30e+00 aAttaTtgtataTCaATATcaacT
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2325 8.10e+01 c.AtCAtGaagAaCc
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2750 3.10e+00 TAaaATCcTTaAcAAaC
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2751 9.60e-01 GgCaTCCcttcTgCGgcGgaC
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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 GSU0951

GSU0951 is enriched for 5 functions in 3 categories.
Module neighborhood information for GSU0951

GSU0951 has total of 54 gene neighbors in modules 82, 296
Gene neighbors (54)
Gene Common Name Description Module membership
GSU0120 GSU0120 hydrogenase maturation protease (VIMSS) 82, 141
GSU0264 GSU0264 drug resistance transporter, Bcr/CflA family (VIMSS) 82, 141
GSU0275 GSU0275 hypothetical protein (VIMSS) 82, 141
GSU0278 GSU0278 outer membrane efflux protein (VIMSS) 82, 141
GSU0291 cheR CheR methyltransferase, SAM binding domain protein, putative (NCBI) 36, 296
GSU0375 gcvT glycine cleavage system T protein (NCBI) 296, 304
GSU0376 gcvH-1 glycine cleavage system H protein (NCBI) 153, 296
GSU0377 GSU0377 glycine cleavage system P protein, subunit 1 (VIMSS) 153, 296
GSU0378 GSU0378 glycine cleavage system P protein, subunit 2 (VIMSS) 153, 296
GSU0379 GSU0379 biotin/lipoate A/B protein ligase family protein (NCBI) 153, 296
GSU0380 lipA lipoic acid synthetase (NCBI) 153, 296
GSU0381 GSU0381 lipoprotein, putative (VIMSS) 274, 296
GSU0382 GSU0382 conserved hypothetical protein (VIMSS) 153, 296
GSU0400 GSU0400 methyl-accepting chemotaxis protein (VIMSS) 82, 156
GSU0425 fliR flagellar biosynthesis protein FliR (NCBI) 82, 141
GSU0426 flhB flagellar biosynthetic protein FlhB (NCBI) 82, 275
GSU0698 GSU0698 PBS lyase HEAT-like repeat protein (NCBI) 296, 304
GSU0766 GSU0766 methyl-accepting chemotaxis protein, putative (VIMSS) 82, 272
GSU0920 GSU0920 hypothetical protein (NCBI) 82, 296
GSU0951 GSU0951 transcriptional regulator, TetR family (VIMSS) 82, 296
GSU1097 pstA phosphate ABC transporter, permease protein (NCBI) 82, 141
GSU1294 GSU1294 methyl-accepting chemotaxis protein (VIMSS) 82, 190
GSU1304 GSU1304 methyl-accepting chemotaxis protein (VIMSS) 82, 155
GSU1315 merA-1 mercuric reductase (NCBI) 296, 304
GSU1326 recG ATP-dependent DNA helicase RecG (NCBI) 296, 298
GSU2160 GSU2160 hypothetical protein (VIMSS) 78, 82
GSU2186 GSU2186 conserved hypothetical protein (VIMSS) 82, 190
GSU2187 GSU2187 ABC transporter, permease protein (VIMSS) 82, 190
GSU2188 GSU2188 ABC transporter, ATP-binding protein (VIMSS) 82, 190
GSU2189 GSU2189 sensor histidine kinase (VIMSS) 82, 190
GSU2299 GSU2299 cytochrome c family protein (NCBI) 82, 141
GSU2336 otsB trehalose-phosphatase (NCBI) 296, 300
GSU2385 GSU2385 hypothetical protein (VIMSS) 82, 278
GSU2388 GSU2388 sensory box histidine kinase (VIMSS) 82, 155
GSU2401 GSU2401 sensory box histidine kinase/response regulator (VIMSS) 82, 141
GSU2466 GSU2466 hypothetical protein (VIMSS) 39, 296
GSU2531 GSU2531 sensory box histidine kinase (VIMSS) 79, 82
GSU2535 GSU2535 response regulator (VIMSS) 82, 224
GSU2573 GSU2573 hypothetical protein (VIMSS) 104, 296
GSU2577 GSU2577 hypothetical protein (VIMSS) 296, 304
GSU2580 GSU2580 hypothetical protein (VIMSS) 82, 141
GSU2671 GSU2671 hypothetical protein (VIMSS) 82, 304
GSU2673 GSU2673 hypothetical protein (VIMSS) 144, 296
GSU2676 GSU2676 membrane protein, putative (VIMSS) 152, 296
GSU2780 GSU2780 hypothetical protein (VIMSS) 165, 296
GSU2781 GSU2781 efflux transporter, RND family, MFP subunit (NCBI) 130, 296
GSU2782 GSU2782 AcrB/AcrD/AcrF family protein (VIMSS) 278, 296
GSU2783 GSU2783 HDIG domain protein (VIMSS) 147, 296
GSU2973 GSU2973 lipoprotein, putative (VIMSS) 59, 296
GSU3053 fliA RNA polymerase sigma factor for flagellar operon (NCBI) 296, 312
GSU3104 prfA peptide chain release factor 1 (NCBI) 82, 140
GSU3154 GSU3154 cytochrome c nitrite reductase, catalytic subunit NrfA, putative (VIMSS) 16, 82
GSU3221 GSU3221 cytochrome c family protein (NCBI) 6, 82
GSU3227 GSU3227 hypothetical protein (VIMSS) 82, 141
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 GSU0951
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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