Organism : Geobacter sulfurreducens | Module List :
GSU3060

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 GSU3060
(Mouseover regulator name to see its description)

GSU3060 is regulated by 17 influences and regulates 15 modules.
Regulators for GSU3060 (17)
Regulator Module Operator
GSU0534 172 tf
GSU0776 172 tf
GSU0963 172 tf
GSU2185 172 tf
GSU2571 172 tf
GSU2670 172 tf
GSU2945 172 tf
GSU3060 172 tf
GSU0732 270 tf
GSU1201 270 tf
GSU1218 270 tf
GSU1419 270 tf
GSU1525 270 tf
GSU1626 270 tf
GSU1692 270 tf
GSU3060 270 tf
GSU3087 270 tf

Warning: GSU3060 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
2504 7.30e-02 TcT.cTTttcggaatGctcGatT
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2505 1.00e+00 CcAgccGAtcCtCccaTCCaTtCa
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2700 2.10e+01 GCttaACaCtcTgaAgcG
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2701 6.10e+00 AgGatcGcCTGgtgcgGgAct
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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 GSU3060

GSU3060 is enriched for 5 functions in 3 categories.
Module neighborhood information for GSU3060

GSU3060 has total of 30 gene neighbors in modules 172, 270
Gene neighbors (30)
Gene Common Name Description Module membership
GSU0066 GSU0066 AhpC/Tsa family protein, selenocysteine-containing (NCBI) 270, 320
GSU0067 GSU0067 carbonic anhydrase (NCBI) 270, 320
GSU0069 GSU0069 oxidoreductase, iron-sulfur cluster-binding subunit (VIMSS) 270, 279
GSU0129 def-1 polypeptide deformylase (NCBI) 60, 172
GSU0130 fmt methionyl-tRNA formyltransferase (NCBI) 172, 321
GSU0131 GSU0131 conserved hypothetical protein (VIMSS) 172, 203
GSU0195 GSU0195 conserved hypothetical protein (VIMSS) 270, 320
GSU0675 GSU0675 hypothetical protein (VIMSS) 2, 270
GSU1168 GSU1168 hypothetical protein (VIMSS) 270, 310
GSU1558 GSU1558 hypothetical protein (VIMSS) 270, 288
GSU1615 GSU1615 membrane protein, putative (VIMSS) 270, 310
GSU1625 GSU1625 hypothetical protein (VIMSS) 172, 190
GSU1646 GSU1646 lipoprotein, putative (VIMSS) 27, 172
GSU1662 GSU1662 hypothetical protein (VIMSS) 137, 270
GSU2015 GSU2015 MutT/nudix family protein (VIMSS) 127, 172
GSU2568 GSU2568 MiaB-like tRNA modifying enzyme (NCBI) 172, 290
GSU2569 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI) 172, 290
GSU2570 spl1 cysteine desulfurase (NCBI) 172, 290
GSU2571 GSU2571 RrF2 family protein (VIMSS) 172, 290
GSU2572 cysE serine acetyltransferase (NCBI) 172, 290
GSU2687 GSU2687 HlyD family secretion protein (NCBI) 211, 270
GSU2688 GSU2688 hypothetical protein (VIMSS) 270, 324
GSU3059 GSU3059 radical SAM domain protein (NCBI) 172, 270
GSU3060 GSU3060 transcriptional regulator, TetR family (VIMSS) 172, 270
GSU3061 shc-2 squalene-hopene cyclase (NCBI) 172, 270
GSU3096 hisA phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI) 172, 203
GSU3097 hisH imidazole glycerol phosphate synthase, glutamine amidotransferase subunit (NCBI) 127, 172
GSU3101 hisG-2 ATP phosphoribosyltransferase (NCBI) 172, 203
GSU3102 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase (NCBI) 172, 203
GSU3328 GSU3328 conserved hypothetical protein (NCBI) 177, 270
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 GSU3060
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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