Organism : Geobacter sulfurreducens | Module List :
GSU0516

conserved hypothetical protein (VIMSS)

CircVis
Functional Annotations (5)
Function System
Sugar phosphate isomerases/epimerases cog/ cog
DNA binding go/ molecular_function
endonuclease activity go/ molecular_function
intracellular go/ cellular_component
DNA repair go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0516
(Mouseover regulator name to see its description)

GSU0516 is regulated by 17 influences and regulates 0 modules.
Regulators for GSU0516 (17)
Regulator Module Operator
GSU0205 331 tf
GSU0366 331 tf
GSU0534 331 tf
GSU0896 331 tf
GSU1410 331 tf
GSU2506 331 tf
GSU2571 331 tf
GSU0175 308 tf
GSU0267 308 tf
GSU0551 308 tf
GSU0776 308 tf
GSU1692 308 tf
GSU1940 308 tf
GSU2262 308 tf
GSU2980 308 tf
GSU3108 308 tf
GSU3396 308 tf

Warning: GSU0516 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
2772 2.20e+00 tgctAttGcTAtgATGCaaTctaA
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2773 1.30e+02 gGgTtCAAcaAtActcGgtAAa
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2818 1.50e+04 Atgaca.aATGCt.T
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2819 1.60e+04 CGGCGCctc.CagG
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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 GSU0516

GSU0516 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Sugar phosphate isomerases/epimerases cog/ cog
DNA binding go/ molecular_function
endonuclease activity go/ molecular_function
intracellular go/ cellular_component
DNA repair go/ biological_process
Module neighborhood information for GSU0516

GSU0516 has total of 28 gene neighbors in modules 308, 331
Gene neighbors (28)
Gene Common Name Description Module membership
GSU0174 GSU0174 acetyl-CoA hydrolase/transferase family protein (VIMSS) 32, 308
GSU0175 GSU0175 transcriptional regulator, TetR family (VIMSS) 32, 308
GSU0230 pilT-2 twitching motility protein PilT (NCBI) 308, 322
GSU0516 GSU0516 conserved hypothetical protein (VIMSS) 308, 331
GSU0697 GSU0697 ceramide glucosyltransferase, putative (VIMSS) 78, 331
GSU0757 GSU0757 lipoprotein, putative (VIMSS) 66, 331
GSU0797 GSU0797 conserved hypothetical protein TIGR00427 (VIMSS) 196, 308
GSU0835 GSU0835 hypothetical protein (VIMSS) 317, 331
GSU0895 GSU0895 GAF domain/GGDEF domain protein (NCBI) 9, 331
GSU0914 rhlE-2 ATP-dependent RNA helicase RhlE (NCBI) 246, 331
GSU1175 tgt-1 queuine tRNA-ribosyltransferase (NCBI) 276, 308
GSU1248 GSU1248 transposase, ISL3 family, truncation (VIMSS) 25, 331
GSU1279 nikMN component of nickel ABCtransport system (Dmitry Rodionov) 231, 331
GSU1280 nikQ component of nickel ABC transport system (Dmitry Rodionov) 231, 331
GSU1408 GSU1408 ParA family protein (VIMSS) 202, 331
GSU1409 GSU1409 NifU-like domain protein (NCBI) 202, 331
GSU1411 GSU1411 sodium/bile acid symporter family protein (VIMSS) 202, 331
GSU1412 GSU1412 hypothetical protein (VIMSS) 202, 331
GSU1575 GSU1575 hypothetical protein (VIMSS) 32, 308
GSU1868 GSU1868 aminotransferase, class V (VIMSS) 249, 308
GSU2243 GSU2243 UDP-N-acetylglucosamine 2-epimerase (VIMSS) 295, 308
GSU2485 GSU2485 potassium transporter family protein (VIMSS) 308, 317
GSU2491 GSU2491 major facilitator family transporter (VIMSS) 216, 331
GSU2785 GSU2785 hypothetical protein (VIMSS) 78, 331
GSU2936 GSU2936 hypothetical protein (VIMSS) 202, 331
GSU2937 GSU2937 cytochrome c family protein (NCBI) 202, 331
GSU2940 GSU2940 lipoprotein, putative (VIMSS) 202, 331
GSU3277 GSU3277 lysM domain protein (NCBI) 176, 308
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 GSU0516
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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