Organism : Geobacter sulfurreducens | Module List :
GSU1129

sigma-54 dependent DNA-binding response regulator (VIMSS)

CircVis
Functional Annotations (9)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1129
(Mouseover regulator name to see its description)

GSU1129 is regulated by 24 influences and regulates 11 modules.
Regulators for GSU1129 (24)
Regulator Module Operator
GSU0013 199 tf
GSU0031 199 tf
GSU1013 199 tf
GSU1218 199 tf
GSU1495 199 tf
GSU1525 199 tf
GSU1569 199 tf
GSU1626 199 tf
GSU1653 199 tf
GSU2581 199 tf
GSU2964 199 tf
GSU3229 199 tf
GSU3457 199 tf
GSU0013 239 tf
GSU0041 239 tf
GSU0896 239 tf
GSU1013 239 tf
GSU1129 239 tf
GSU1218 239 tf
GSU1525 239 tf
GSU1989 239 tf
GSU1992 239 tf
GSU2149 239 tf
GSU3045 239 tf

Warning: GSU1129 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
2558 4.30e-02 aAAccgggctatAgTAGCagAgga
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2559 1.70e-01 ctCctCtGat.gGcctgAtACatA
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2638 2.50e+00 tTtgCCt.tGCAaaGCcaTctaC
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2639 2.80e-02 AagtgTA.CAgAgccCC.tC..GC
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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 GSU1129

GSU1129 is enriched for 9 functions in 3 categories.
Module neighborhood information for GSU1129

GSU1129 has total of 30 gene neighbors in modules 199, 239
Gene neighbors (30)
Gene Common Name Description Module membership
GSU0486 ilvA threonine dehydratase (NCBI) 196, 239
GSU0489 GSU0489 Mg chelatase-related protein (VIMSS) 227, 239
GSU1089 GSU1089 iron-sulfur cluster-binding protein (VIMSS) 196, 239
GSU1129 GSU1129 sigma-54 dependent DNA-binding response regulator (VIMSS) 199, 239
GSU1130 GSU1130 chromosome segregation SMC protein, putative (VIMSS) 199, 239
GSU1131 GSU1131 conserved hypothetical protein (VIMSS) 199, 239
GSU1174 mazG mazG protein (NCBI) 207, 239
GSU1195 GSU1195 HD domain protein (VIMSS) 199, 212
GSU1358 GSU1358 conserved hypothetical protein (VIMSS) 199, 212
GSU1364 GSU1364 HNH endonuclease family protein (NCBI) 199, 338
GSU1433 GSU1433 peptide ABC transporter, periplasmic peptide-binding protein (VIMSS) 52, 239
GSU1489 GSU1489 membrane protein, putative (VIMSS) 75, 199
GSU1513 GSU1513 conserved domain protein (NCBI) 199, 316
GSU1514 GSU1514 heptosyltransferase family protein (VIMSS) 29, 199
GSU1694 GSU1694 hydrolase, haloacid dehalogenase-like family (VIMSS) 111, 239
GSU1859 GSU1859 keto/oxoacid ferredoxin oxidoreductase, gamma subunit (VIMSS) 199, 239
GSU1860 GSU1860 keto/oxoacid ferredoxin oxidoreductase, alpha subunit (VIMSS) 170, 239
GSU1861 GSU1861 keto/oxoacid ferredoxin oxidoreductase, beta subunit (VIMSS) 170, 199
GSU1862 GSU1862 keto/oxoacid ferredoxin oxidoreductase subunit (VIMSS) 199, 239
GSU1864 ksgA dimethyladenosine transferase (NCBI) 199, 249
GSU1865 gcp metalloendopeptidase, putative, glycoprotease family (NCBI) 199, 249
GSU1869 GSU1869 lipoprotein, putative (VIMSS) 199, 249
GSU1871 GSU1871 ribonucleoside-diphosphate reductase, putative (NCBI) 168, 199
GSU1872 GSU1872 hypothetical protein (VIMSS) 199, 209
GSU1931 GSU1931 hypothetical protein (VIMSS) 239, 332
GSU2090 GSU2090 hypothetical protein (NCBI) 91, 239
GSU2105 GSU2105 hypothetical protein (VIMSS) 52, 239
GSU2106 GSU2106 hypothetical protein (VIMSS) 199, 301
GSU3377 GSU3377 helix-hairpin-helix domain protein (NCBI) 239, 328
GSU3380 gatB glutamyl-tRNA(Gln) amidotransferase, B subunit (NCBI) 91, 239
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 GSU1129
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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