Organism : Geobacter sulfurreducens | Module List :
GSU2953 arsC

arsenate reductase (NCBI)

CircVis
Functional Annotations (4)
Function System
Protein-tyrosine-phosphatase cog/ cog
protein tyrosine phosphatase activity go/ molecular_function
protein dephosphorylation go/ biological_process
arsenate reductase (glutaredoxin) activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2953
(Mouseover regulator name to see its description)

GSU2953 is regulated by 14 influences and regulates 0 modules.
Regulators for GSU2953 arsC (14)
Regulator Module Operator
GSU0280 336 tf
GSU0776 336 tf
GSU0812 336 tf
GSU1495 336 tf
GSU1569 336 tf
GSU2033 336 tf
GSU2113 336 tf
GSU2506 336 tf
GSU3363 336 tf
GSU0836 317 tf
GSU0896 317 tf
GSU1495 317 tf
GSU2149 317 tf
GSU2506 317 tf

Warning: GSU2953 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
2790 5.10e+01 gGGAaaAA
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2791 1.10e+03 AAAaAaTAACT
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2828 1.70e+02 aTagttTAa.gTa.caagT
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2829 9.20e+03 acAAGcaTaaCccgAtT
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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 GSU2953

GSU2953 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Protein-tyrosine-phosphatase cog/ cog
protein tyrosine phosphatase activity go/ molecular_function
protein dephosphorylation go/ biological_process
arsenate reductase (glutaredoxin) activity go/ molecular_function
Module neighborhood information for GSU2953

GSU2953 has total of 43 gene neighbors in modules 317, 336
Gene neighbors (43)
Gene Common Name Description Module membership
GSU0053 GSU0053 hypothetical protein (VIMSS) 41, 317
GSU0151 argD acetylornithine aminotransferase (NCBI) 107, 336
GSU0166 GSU0166 hypothetical protein (VIMSS) 312, 336
GSU0271 glmU UDP-N-acetylglucosamine pyrophosphorylase (NCBI) 144, 336
GSU0318 GSU0318 peptidase, M48 family (NCBI) 99, 336
GSU0399 GSU0399 transcriptional regulator, ArsR family (VIMSS) 94, 336
GSU0439 GSU0439 4-hydroxybenzoate octaprenyltransferase, putative (VIMSS) 107, 317
GSU0475 GSU0475 sensory box histidine kinase (VIMSS) 235, 317
GSU0494 GSU0494 iron-sulfur cluster-binding protein (VIMSS) 133, 336
GSU0695 GSU0695 hypothetical protein (VIMSS) 317, 336
GSU0756 GSU0756 methyl-accepting chemotaxis protein (VIMSS) 122, 317
GSU0835 GSU0835 hypothetical protein (VIMSS) 317, 331
GSU0836 GSU0836 nucleoside diphosphate kinase regulator protein, putative (VIMSS) 208, 317
GSU0886 GSU0886 radical SAM domain protein (NCBI) 113, 336
GSU0903 GSU0903 None 126, 317
GSU1094 GSU1094 hypothetical protein (VIMSS) 336, 337
GSU1220 GSU1220 response regulator (VIMSS) 189, 336
GSU1392 GSU1392 CRISPR-associated protein Cas1 (NCBI) 249, 336
GSU1535 recD exodeoxyribonuclease V, alpha subunit (NCBI) 126, 336
GSU2230 holB DNA polymerase III, delta prime subunit (NCBI) 184, 336
GSU2345 GSU2345 rsbU-related protein (VIMSS) 220, 317
GSU2394 GSU2394 hypothetical protein (VIMSS) 321, 336
GSU2441 GSU2441 conserved hypothetical protein (VIMSS) 287, 317
GSU2478 GSU2478 hypothetical protein (VIMSS) 6, 317
GSU2485 GSU2485 potassium transporter family protein (VIMSS) 308, 317
GSU2523 GSU2523 transcriptional regulator, LysR family (VIMSS) 137, 317
GSU2720 hoxU NAD-reducing hydrogenase, gamma subunit (NCBI) 113, 336
GSU2815 GSU2815 sensory box histidine kinase (VIMSS) 97, 317
GSU2900 GSU2900 hypothetical protein (VIMSS) 115, 317
GSU2932 GSU2932 cytochrome b/b6 (VIMSS) 302, 336
GSU2952 GSU2952 transcriptional regulator, ArsR family (VIMSS) 146, 317
GSU2953 arsC arsenate reductase (NCBI) 317, 336
GSU3266 GSU3266 DNA helicase II, putative (VIMSS) 317, 318
GSU3267 GSU3267 hypothetical protein (VIMSS) 241, 317
GSU3268 feoB-2 ferrous iron transport protein B (NCBI) 241, 317
GSU3270 feoA feoA component of ferrous iron transporter (Dmitry Rodionov) 241, 317
GSU3271 GSU3271 hypothetical protein (VIMSS) 241, 317
GSU3319 ppiA peptidyl-prolyl cis-trans isomerase A (NCBI) 97, 317
GSU3373 sun Sun protein (NCBI) 160, 336
GSU3386 GSU3386 lipoprotein, putative (VIMSS) 327, 336
GSU3429 nuoN-2 NADH dehydrogenase I, N subunit (NCBI) 144, 336
GSU3431 nuoL-2 NADH dehydrogenase I, L subunit (NCBI) 283, 336
GSU3456 def-2 polypeptide deformylase (NCBI) 107, 336
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 GSU2953
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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