Organism : Geobacter sulfurreducens | Module List :
GSU1016

potassium uptake protein, Trk family (VIMSS)

CircVis
Functional Annotations (4)
Function System
Predicted permease cog/ cog
potassium ion transport go/ biological_process
cation transmembrane transporter activity go/ molecular_function
YidE_YbjL_dupl tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1016
(Mouseover regulator name to see its description)

GSU1016 is regulated by 26 influences and regulates 0 modules.
Regulators for GSU1016 (26)
Regulator Module Operator
GSU0175 319 tf
GSU0187 319 tf
GSU0254 319 tf
GSU0266 319 tf
GSU0399 319 tf
GSU0551 319 tf
GSU0770 319 tf
GSU1277 319 tf
GSU1382 319 tf
GSU1495 319 tf
GSU1692 319 tf
GSU1940 319 tf
GSU0254 213 tf
GSU0473 213 tf
GSU0812 213 tf
GSU1013 213 tf
GSU1320 213 tf
GSU1382 213 tf
GSU1569 213 tf
GSU1831 213 tf
GSU2033 213 tf
GSU2362 213 tf
GSU2670 213 tf
GSU2915 213 tf
GSU3324 213 tf
GSU3396 213 tf

Warning: GSU1016 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
2586 1.30e+04 AACAaGGA
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2587 4.40e+04 AAATTGTTGT
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2794 2.00e+03 TaACagaAaA
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2795 1.20e+04 AATTcAcAAaaTaa
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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 GSU1016

GSU1016 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted permease cog/ cog
potassium ion transport go/ biological_process
cation transmembrane transporter activity go/ molecular_function
YidE_YbjL_dupl tigr/ tigrfam
Module neighborhood information for GSU1016

GSU1016 has total of 40 gene neighbors in modules 213, 319
Gene neighbors (40)
Gene Common Name Description Module membership
GSU0062 GSU0062 TraD protein, putative (VIMSS) 189, 319
GSU0168 GSU0168 Fic family protein (NCBI) 118, 319
GSU0256 GSU0256 conserved hypothetical protein (NCBI) 88, 319
GSU0302 GSU0302 hypothetical protein (VIMSS) 145, 319
GSU0355 GSU0355 hypothetical protein (VIMSS) 118, 319
GSU0630 GSU0630 conserved domain protein (NCBI) 68, 213
GSU0796 GSU0796 acyl-CoA thioester hydrolase, putative (NCBI) 213, 222
GSU0815 GSU0815 mce-related protein (VIMSS) 30, 213
GSU0889 GSU0889 Acylphosphatase (VIMSS) 213, 226
GSU1012 GSU1012 membrane protein, putative (VIMSS) 213, 283
GSU1016 GSU1016 potassium uptake protein, Trk family (VIMSS) 213, 319
GSU1223 GSU1223 hypothetical protein (VIMSS) 106, 319
GSU1229 GSU1229 lipoprotein, putative (VIMSS) 173, 213
GSU1432 GSU1432 TPR domain protein (VIMSS) 213, 231
GSU1486 GSU1486 MttB family protein (VIMSS) 319, 338
GSU1546 GSU1546 hypothetical protein (VIMSS) 68, 319
GSU1547 GSU1547 TPR domain protein (NCBI) 213, 224
GSU1566 GSU1566 hypothetical protein (VIMSS) 213, 232
GSU1719 GSU1719 hypothetical protein (VIMSS) 30, 213
GSU1724 GSU1724 nuclease SbcCD, D subunit, putative (NCBI) 213, 282
GSU1841 GSU1841 membrane protein, putative (NCBI) 98, 319
GSU1842 GSU1842 polysaccharide biosynthesis/export domain protein (NCBI) 98, 319
GSU1845 GSU1845 hypothetical protein (VIMSS) 191, 319
GSU1936 nadC nicotinate-nucleotide pyrophosphorylase (NCBI) 213, 282
GSU1942 GSU1942 UDP-glucose/GDP-mannose dehydrogenase family protein (VIMSS) 189, 319
GSU1958 GSU1958 polysaccharide deacetylase domain protein (NCBI) 213, 232
GSU2145 vicR DNA-binding response regulator (NCBI) 294, 319
GSU2146 GSU2146 conserved hypothetical protein (VIMSS) 166, 319
GSU2147 GSU2147 cadmium-translocating P-type ATPase (VIMSS) 166, 319
GSU2152 GSU2152 hypothetical protein (VIMSS) 1, 213
GSU2211 GSU2211 hypothetical protein (VIMSS) 309, 319
GSU2278 prfB peptide chain release factor 2 (NCBI) 198, 213
GSU2315 GSU2315 hypothetical protein (VIMSS) 200, 319
GSU2398 GSU2398 conserved hypothetical protein (VIMSS) 68, 319
GSU2500 GSU2500 hypothetical protein (NCBI) 92, 213
GSU2542 GSU2542 hypothetical protein (VIMSS) 213, 217
GSU2699 GSU2699 molybdopterin converting factor, subunit 2 (NCBI) 166, 319
GSU2700 GSU2700 tungstate ABC transporter, periplasmic tungstate-binding protein, putative (NCBI) 114, 319
GSU2959 GSU2959 membrane protein, putative (NCBI) 14, 213
GSU3186 GSU3186 conserved hypothetical protein (VIMSS) 213, 300
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 GSU1016
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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