Organism : Geobacter sulfurreducens | Module List :
GSU1013

chemotaxis MotB protein, putative (VIMSS)

CircVis
Functional Annotations (9)
Function System
Flagellar motor protein cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
cell outer membrane go/ cellular_component
sequence-specific DNA binding go/ molecular_function
protein dimerization activity go/ molecular_function
Bacterial chemotaxis kegg/ kegg pathway
Flagellar assembly kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1013
(Mouseover regulator name to see its description)

GSU1013 is regulated by 20 influences and regulates 38 modules.
Regulators for GSU1013 (20)
Regulator Module Operator
GSU0041 85 tf
GSU0732 85 tf
GSU1013 85 tf
GSU1218 85 tf
GSU1495 85 tf
GSU1626 85 tf
GSU1992 85 tf
GSU2149 85 tf
GSU2581 85 tf
GSU3041 85 tf
GSU3421 85 tf
GSU0187 311 tf
GSU1013 311 tf
GSU1218 311 tf
GSU1495 311 tf
GSU1522 311 tf
GSU1525 311 tf
GSU1626 311 tf
GSU1934 311 tf
GSU2523 311 tf

Warning: GSU1013 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
2330 5.20e+02 tGt.aaaac.gtaCcaTGaAt
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2331 1.50e+04 TtcCTCCTtga
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2778 1.90e+00 aATgGtaccAcAGGgat
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2779 1.20e+01 tAgctTCAggCAaAGtAaA
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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 GSU1013

GSU1013 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Flagellar motor protein cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
nucleus go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
cell outer membrane go/ cellular_component
sequence-specific DNA binding go/ molecular_function
protein dimerization activity go/ molecular_function
Bacterial chemotaxis kegg/ kegg pathway
Flagellar assembly kegg/ kegg pathway
Module neighborhood information for GSU1013

GSU1013 has total of 31 gene neighbors in modules 85, 311
Gene neighbors (31)
Gene Common Name Description Module membership
GSU0139 GSU0139 hypothetical protein (VIMSS) 93, 311
GSU0144 GSU0144 sensory box histidine kinase (VIMSS) 53, 85
GSU0241 GSU0241 BchE/P-methylase family protein (VIMSS) 119, 311
GSU0244 GSU0244 radical SAM domain protein (NCBI) 119, 311
GSU0478 GSU0478 conserved hypothetical protein (VIMSS) 85, 235
GSU0479 aspA aspartate ammonia-lyase (NCBI) 85, 235
GSU0481 GSU0481 hypothetical protein (VIMSS) 85, 235
GSU0681 GSU0681 sensory box histidine kinase (VIMSS) 53, 85
GSU0717 GSU0717 hypothetical protein (VIMSS) 85, 310
GSU0719 GSU0719 hypothetical protein (VIMSS) 27, 311
GSU0720 GSU0720 desulfoferrodoxin ferrous iron-binding domain (NCBI) 85, 311
GSU1013 GSU1013 chemotaxis MotB protein, putative (VIMSS) 85, 311
GSU1160 GSU1160 hypothetical protein (VIMSS) 85, 310
GSU1307 ftn ferritin (NCBI) 27, 85
GSU1448 GSU1448 PHP domain protein (NCBI) 85, 127
GSU2142 GSU2142 hypothetical protein (VIMSS) 97, 311
GSU2321 GSU2321 hypothetical protein (VIMSS) 175, 311
GSU2356 GSU2356 hypothetical protein (VIMSS) 7, 311
GSU2424 GSU2424 hypothetical protein (VIMSS) 85, 134
GSU2486 GSU2486 conserved hypothetical protein (VIMSS) 257, 311
GSU2488 GSU2488 conserved hypothetical protein (NCBI) 73, 311
GSU2586 GSU2586 hypothetical protein (VIMSS) 288, 311
GSU2633 GSU2633 lipoprotein, putative (VIMSS) 23, 311
GSU2675 GSU2675 hypothetical protein (VIMSS) 85, 165
GSU2691 GSU2691 conserved hypothetical protein (VIMSS) 27, 85
GSU2968 GSU2968 hypothetical protein (VIMSS) 85, 216
GSU3131 GSU3131 hypothetical protein (VIMSS) 85, 166
GSU3152 GSU3152 sensory box protein (VIMSS) 85, 188
GSU3326 GSU3326 conserved hypothetical protein (VIMSS) 27, 311
GSU3327 GSU3327 conserved hypothetical protein (VIMSS) 27, 85
GSU3388 GSU3388 membrane protein, putative (VIMSS) 23, 311
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 GSU1013
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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