Organism : Geobacter sulfurreducens | Module List :
GSU2741

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 GSU2741
(Mouseover regulator name to see its description)

GSU2741 is regulated by 11 influences and regulates 12 modules.
Regulators for GSU2741 (11)
Regulator Module Operator
GSU0372 66 tf
GSU0551 66 tf
GSU0770 66 tf
GSU2237 66 tf
GSU3087 66 tf
GSU0300 6 tf
GSU1626 6 tf
GSU2202 6 tf
GSU2540 6 tf
GSU2666 6 tf
GSU2716 6 tf

Warning: GSU2741 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
2172 1.50e+01 AAttCAATtT
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2173 1.30e+04 AAAaGGTGTTATATTTttaTTGAA
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2292 1.80e+03 CagtgttcTaatGAactAATaGaG
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2293 3.00e+03 cGGgc.AGGgGgtTG
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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 GSU2741

GSU2741 is enriched for 5 functions in 3 categories.
Module neighborhood information for GSU2741

GSU2741 has total of 44 gene neighbors in modules 6, 66
Gene neighbors (44)
Gene Common Name Description Module membership
GSU0039 GSU0039 hypothetical protein (VIMSS) 66, 124
GSU0214 GSU0214 conserved hypothetical protein (VIMSS) 6, 95
GSU0357 GSU0357 cytochrome c family protein (VIMSS) 6, 95
GSU0402 GSU0402 hemerythrin family protein (NCBI) 6, 235
GSU0542 GSU0542 GGDEF domain protein (NCBI) 9, 66
GSU0590 GSU0590 hypothetical protein (VIMSS) 6, 250
GSU0598 GSU0598 sigma-54 dependent DNA-binding response regulator (VIMSS) 66, 269
GSU0757 GSU0757 lipoprotein, putative (VIMSS) 66, 331
GSU0822 GSU0822 sensory box histidine kinase (VIMSS) 6, 141
GSU1251 GSU1251 BNR repeat domain protein (VIMSS) 66, 104
GSU1252 GSU1252 conserved domain protein (NCBI) 66, 104
GSU1253 GSU1253 hypothetical protein (VIMSS) 66, 104
GSU1254 GSU1254 hypothetical protein (VIMSS) 6, 104
GSU1256 GSU1256 conserved domain protein (NCBI) 6, 95
GSU1677 GSU1677 AMP-binding enzyme/acyltransferase (NCBI) 57, 66
GSU1853 GSU1853 membrane protein, putative (VIMSS) 66, 124
GSU1854 GSU1854 UDP-glucose/GDP-mannose dehydrogenase family protein (VIMSS) 66, 124
GSU1855 GSU1855 capsule polysaccharide export protein, putative (VIMSS) 66, 124
GSU2131 GSU2131 hypothetical protein (VIMSS) 51, 66
GSU2151 ssb-1 single-strand binding protein (NCBI) 6, 70
GSU2159 GSU2159 hypothetical protein (VIMSS) 6, 253
GSU2203 GSU2203 cytochrome c family protein (VIMSS) 6, 269
GSU2355 GSU2355 hypothetical protein (VIMSS) 6, 135
GSU2478 GSU2478 hypothetical protein (VIMSS) 6, 317
GSU2479 GSU2479 hypothetical protein (VIMSS) 6, 9
GSU2499 GSU2499 hypothetical protein (VIMSS) 66, 341
GSU2501 GSU2501 cytochrome c family protein (NCBI) 66, 341
GSU2503 GSU2503 cytochrome c family protein (NCBI) 6, 66
GSU2504 GSU2504 cytochrome c family protein (NCBI) 6, 60
GSU2505 GSU2505 NHL repeat domain protein (VIMSS) 66, 341
GSU2508 GSU2508 TPR domain protein (NCBI) 6, 341
GSU2640 GSU2640 hypothetical protein (VIMSS) 66, 95
GSU2641 GSU2641 hypothetical protein (VIMSS) 66, 95
GSU2711 GSU2711 hypothetical protein (VIMSS) 6, 220
GSU2735 GSU2735 transcriptional regulator, TetR family (NCBI) 65, 66
GSU2741 GSU2741 transcriptional regulator, TetR family (VIMSS) 6, 66
GSU2763 GSU2763 conserved hypothetical protein (VIMSS) 4, 66
GSU2784 GSU2784 hypothetical protein (VIMSS) 6, 252
GSU2895 GSU2895 hypothetical protein (VIMSS) 6, 66
GSU2896 GSU2896 ankyrin-related protein (VIMSS) 6, 95
GSU3030 GSU3030 hypothetical protein (VIMSS) 6, 141
GSU3221 GSU3221 cytochrome c family protein (NCBI) 6, 82
GSU3313 GSU3313 thiolase, putative (NCBI) 9, 66
GSU3420 GSU3420 lipid A biosynthesis lauroyl acyltransferase, putative (VIMSS) 9, 66
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 GSU2741
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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