Organism : Geobacter sulfurreducens | Module List :
GSU1220

response regulator (VIMSS)

CircVis
Functional Annotations (6)
Function System
FOG: CheY-like receiver cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
transport go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1220
(Mouseover regulator name to see its description)

GSU1220 is regulated by 18 influences and regulates 0 modules.
Regulators for GSU1220 (18)
Regulator Module Operator
GSU0254 189 tf
GSU0266 189 tf
GSU0372 189 tf
GSU1115 189 tf
GSU1268 189 tf
GSU1940 189 tf
GSU2033 189 tf
GSU2915 189 tf
GSU3087 189 tf
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

Warning: GSU1220 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
2538 7.60e+04 ttcCgt.CCT.tT.tT.aTcgag
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2539 5.10e+04 AtccGtTcatccTgA
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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 GSU1220

GSU1220 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
FOG: CheY-like receiver cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
transport go/ biological_process
Module neighborhood information for GSU1220

GSU1220 has total of 50 gene neighbors in modules 189, 336
Gene neighbors (50)
Gene Common Name Description Module membership
GSU0062 GSU0062 TraD protein, putative (VIMSS) 189, 319
GSU0150 argB acetylglutamate kinase (NCBI) 107, 189
GSU0151 argD acetylornithine aminotransferase (NCBI) 107, 336
GSU0166 GSU0166 hypothetical protein (VIMSS) 312, 336
GSU0206 GSU0206 ZIP zinc transporter family protein (VIMSS) 189, 206
GSU0231 GSU0231 hypothetical protein (VIMSS) 189, 224
GSU0271 glmU UDP-N-acetylglucosamine pyrophosphorylase (NCBI) 144, 336
GSU0318 GSU0318 peptidase, M48 family (NCBI) 99, 336
GSU0330 GSU0330 general secretion pathway protein C, putative (NCBI) 173, 189
GSU0399 GSU0399 transcriptional regulator, ArsR family (VIMSS) 94, 336
GSU0494 GSU0494 iron-sulfur cluster-binding protein (VIMSS) 133, 336
GSU0695 GSU0695 hypothetical protein (VIMSS) 317, 336
GSU0848 GSU0848 ferredoxin family protein, putative (VIMSS) 21, 189
GSU0886 GSU0886 radical SAM domain protein (NCBI) 113, 336
GSU1015 GSU1015 hypothetical protein (VIMSS) 21, 189
GSU1035 GSU1035 methyl-accepting chemotaxis protein (NCBI) 57, 189
GSU1065 GSU1065 hypothetical protein (VIMSS) 173, 189
GSU1085 GSU1085 hypothetical protein (VIMSS) 57, 189
GSU1094 GSU1094 hypothetical protein (VIMSS) 336, 337
GSU1142 cheW-3 purine-binding chemotaxis protein CheW (NCBI) 189, 241
GSU1163 GSU1163 ABC transporter, permease protein (VIMSS) 189, 266
GSU1220 GSU1220 response regulator (VIMSS) 189, 336
GSU1392 GSU1392 CRISPR-associated protein Cas1 (NCBI) 249, 336
GSU1395 GSU1395 hypothetical protein (VIMSS) 57, 189
GSU1535 recD exodeoxyribonuclease V, alpha subunit (NCBI) 126, 336
GSU1577 cobO cob(I)alamin adenosyltransferase (NCBI) 189, 231
GSU1942 GSU1942 UDP-glucose/GDP-mannose dehydrogenase family protein (VIMSS) 189, 319
GSU2013 GSU2013 phosphoglucomutase/phosphomannomutase family protein (VIMSS) 55, 189
GSU2118 GSU2118 integrative genetic element Gsu21, integrase (VIMSS) 189, 307
GSU2137 GSU2137 metal ion efflux outer membrane protein family protein, putative (VIMSS) 110, 189
GSU2175 GSU2175 trfA-related protein (VIMSS) 71, 189
GSU2230 holB DNA polymerase III, delta prime subunit (NCBI) 184, 336
GSU2302 GSU2302 trehalose-phosphatase, putative (VIMSS) 20, 189
GSU2386 GSU2386 methylcobamide:CoM methyltransferase-related protein (NCBI) 189, 266
GSU2393 GSU2393 ISGsu5, transposase, truncation (VIMSS) 121, 189
GSU2394 GSU2394 hypothetical protein (VIMSS) 321, 336
GSU2719 hoxY NAD-reducing hydrogenase, delta subunit (NCBI) 189, 224
GSU2720 hoxU NAD-reducing hydrogenase, gamma subunit (NCBI) 113, 336
GSU2932 GSU2932 cytochrome b/b6 (VIMSS) 302, 336
GSU2953 arsC arsenate reductase (NCBI) 317, 336
GSU3116 GSU3116 1-acyl-sn-glycerol-3-phosphate acyltransferase, putative (NCBI) 81, 189
GSU3198 cheY-7 chemotaxis protein CheY (NCBI) 189, 326
GSU3202 GSU3202 hypothetical protein (VIMSS) 189, 326
GSU3364 GSU3364 hypothetical protein (VIMSS) 81, 189
GSU3373 sun Sun protein (NCBI) 160, 336
GSU3386 GSU3386 lipoprotein, putative (VIMSS) 327, 336
GSU3428 GSU3428 cytochrome c family protein, putative (NCBI) 189, 318
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 GSU1220
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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