Organism : Geobacter sulfurreducens | Module List :
GSU0234

transporter, FNT family (VIMSS)

CircVis
Functional Annotations (6)
Function System
Formate/nitrite family of transporters cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
formate dehydrogenase (NAD+) activity go/ molecular_function
formate dehydrogenase complex go/ cellular_component
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0234
(Mouseover regulator name to see its description)

GSU0234 is regulated by 18 influences and regulates 0 modules.
Regulators for GSU0234 (18)
Regulator Module Operator
GSU0300 322 tf
GSU0359 322 tf
GSU0473 322 tf
GSU0551 322 tf
GSU0735 322 tf
GSU2506 322 tf
GSU2587 322 tf
GSU3087 322 tf
GSU3217 322 tf
GSU0164 224 tf
GSU0473 224 tf
GSU1095 224 tf
GSU1115 224 tf
GSU1250 224 tf
GSU1522 224 tf
GSU2581 224 tf
GSU2787 224 tf
GSU2915 224 tf

Warning: GSU0234 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
2608 1.30e+03 ccATcGaCcgG
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2609 5.20e+04 GcaaCcctTccagaaCAcCtAT
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2800 7.00e+02 CTCCTc
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2801 9.80e+03 ccGatt.TC.ctGtttactgta
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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 GSU0234

GSU0234 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Formate/nitrite family of transporters cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
formate dehydrogenase (NAD+) activity go/ molecular_function
formate dehydrogenase complex go/ cellular_component
membrane go/ cellular_component
Module neighborhood information for GSU0234

GSU0234 has total of 38 gene neighbors in modules 224, 322
Gene neighbors (38)
Gene Common Name Description Module membership
GSU0230 pilT-2 twitching motility protein PilT (NCBI) 308, 322
GSU0231 GSU0231 hypothetical protein (VIMSS) 189, 224
GSU0234 GSU0234 transporter, FNT family (VIMSS) 224, 322
GSU0308 hypD hydrogenase expression/formation protein HypD (NCBI) 44, 322
GSU0372 GSU0372 sigma-54 dependent DNA-binding response regulator (VIMSS) 224, 304
GSU0412 GSU0412 flagellar assembly protein fliH, putative (VIMSS) 186, 322
GSU0502 GSU0502 lipoprotein, putative (VIMSS) 130, 322
GSU0573 GSU0573 alcohol dehydrogenase, zinc-containing (VIMSS) 295, 322
GSU0799 GSU0799 amino acid ABC transporter, permease protein (NCBI) 196, 224
GSU0876 GSU0876 diacylglycerol kinase catalytic domain protein (NCBI) 89, 322
GSU0878 GSU0878 glycosyl transferase, group 2 family protein (NCBI) 63, 224
GSU0885 GSU0885 cobyrinic acid a,c-diamide synthase family protein (NCBI) 224, 274
GSU0948 GSU0948 ABC transporter, permease protein, putative (VIMSS) 9, 224
GSU1037 GSU1037 sensory box/response regulator (VIMSS) 1, 224
GSU1188 GSU1188 rhomboid family protein (VIMSS) 204, 224
GSU1547 GSU1547 TPR domain protein (NCBI) 213, 224
GSU1616 dinP ImpB/MucB/SamB family protein (NCBI) 269, 322
GSU1671 GSU1671 response regulator/GGDEF domain protein (NCBI) 59, 224
GSU1714 GSU1714 BRO family protein, truncation (VIMSS) 110, 224
GSU2096 GSU2096 iron-sulfur cluster-binding protein (VIMSS) 113, 322
GSU2158 norQ cobS protein, putative (NCBI) 1, 322
GSU2162 GSU2162 hypothetical protein (VIMSS) 1, 224
GSU2359 GSU2359 hypothetical protein (VIMSS) 63, 224
GSU2368 folC folC bifunctional protein (NCBI) 224, 318
GSU2375 GSU2375 None 126, 322
GSU2533 GSU2533 hypothetical protein (VIMSS) 224, 278
GSU2535 GSU2535 response regulator (VIMSS) 82, 224
GSU2591 GSU2591 ISGsu5, transposase (VIMSS) 322, 337
GSU2705 moaB molybdenum cofactor biosynthesis protein B (NCBI) 175, 224
GSU2719 hoxY NAD-reducing hydrogenase, delta subunit (NCBI) 189, 224
GSU2787 GSU2787 transcriptional regulator, LysR family (VIMSS) 95, 224
GSU2942 GSU2942 methyl-accepting chemotaxis protein (VIMSS) 186, 224
GSU2974 GSU2974 methylenetetrahydrofolate reductase family protein (VIMSS) 224, 322
GSU3028 motB chemotaxis MotB protein (NCBI) 322, 337
GSU3121 GSU3121 EF hand domain protein (VIMSS) 1, 224
GSU3166 GSU3166 conserved hypothetical protein (VIMSS) 130, 322
GSU3228 GSU3228 cytochrome c family protein (VIMSS) 34, 224
GSU3316 GSU3316 cytochrome c biogenesis protein, CcmF/CcyK/CcsA family (VIMSS) 15, 224
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 GSU0234
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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