Organism : Geobacter sulfurreducens | Module List :
GSU1727

dnaK suppressor, putative (VIMSS)

CircVis
Functional Annotations (2)
Function System
DnaK suppressor protein cog/ cog
zinc ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1727
(Mouseover regulator name to see its description)

GSU1727 is regulated by 21 influences and regulates 38 modules.
Regulators for GSU1727 (21)
Regulator Module Operator
GSU0732 339 tf
GSU1013 339 tf
GSU1522 339 tf
GSU1525 339 tf
GSU1626 339 tf
GSU1639 339 tf
GSU1727 339 tf
GSU1934 339 tf
GSU1989 339 tf
GSU2581 339 tf
GSU0366 188 tf
GSU1013 188 tf
GSU1483 188 tf
GSU1522 188 tf
GSU1525 188 tf
GSU1727 188 tf
GSU1992 188 tf
GSU2149 188 tf
GSU2237 188 tf
GSU2262 188 tf
GSU2831 188 tf

Warning: GSU1727 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
2536 6.30e+00 ttgaGcatTtTtTcAaCaatttA
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2537 6.70e+03 AaAC.cGgAAcgaAaagGGaG
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2834 1.40e+01 aCaaAg.Ca...GTCg.T.tGGaa
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2835 2.00e+02 aaGCctTaCGCaTcgTcccGCcGt
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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 GSU1727

GSU1727 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
DnaK suppressor protein cog/ cog
zinc ion binding go/ molecular_function
Module neighborhood information for GSU1727

GSU1727 has total of 26 gene neighbors in modules 188, 339
Gene neighbors (26)
Gene Common Name Description Module membership
GSU0051 GSU0051 CRISPR-associated HD domain protein (NCBI) 188, 244
GSU0188 GSU0188 conserved domain protein (VIMSS) 294, 339
GSU0193 GSU0193 L-sorbosone dehydrogenase, putative (NCBI) 182, 339
GSU0194 GSU0194 conserved hypothetical protein (VIMSS) 182, 339
GSU0200 iorA isoquinoline 1-oxidoreductase, alpha subunit (NCBI) 188, 261
GSU0202 GSU0202 conserved hypothetical protein (NCBI) 178, 339
GSU0696 GSU0696 glucose 1-dehydrogenase (VIMSS) 188, 280
GSU0802 GSU0802 oxidoreductase, short chain dehydrogenase/reductase family (NCBI) 182, 339
GSU0810 GSU0810 OmpA domain protein (VIMSS) 288, 339
GSU0907 GSU0907 thiF family protein (NCBI) 175, 339
GSU0910 GSU0910 aldehyde:ferredoxin oxidoreductase, tungsten-containing (VIMSS) 182, 339
GSU1209 GSU1209 conserved hypothetical protein (VIMSS) 177, 188
GSU1306 GSU1306 PHP domain protein (NCBI) 118, 188
GSU1727 GSU1727 dnaK suppressor, putative (VIMSS) 188, 339
GSU2148 GSU2148 hypothetical protein (VIMSS) 188, 280
GSU2536 GSU2536 dienelactone hydrolase family protein (VIMSS) 188, 280
GSU2656 aceF pyruvate dehydrogenase complex E2 component, dihydrolipoamide acetyltransferase (NCBI) 261, 339
GSU2657 cotA spore coat protein A (NCBI) 165, 188
GSU2728 GSU2728 hypothetical protein (VIMSS) 261, 339
GSU2910 GSU2910 hypothetical protein (VIMSS) 166, 188
GSU3076 GSU3076 cell division protein FtsL, putative (NCBI) 188, 200
GSU3152 GSU3152 sensory box protein (VIMSS) 85, 188
GSU3251 GSU3251 conserved hypothetical protein (VIMSS) 188, 251
GSU3256 galT galactose-1-phosphate uridylyltransferase (NCBI) 188, 279
GSU3357 GSU3357 sensory box histidine kinase (VIMSS) 211, 339
GSU3359 GSU3359 conserved hypothetical protein (VIMSS) 261, 339
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 GSU1727
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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