Organism : Geobacter sulfurreducens | Module List :
GSU0359

sensory box protein/sigma-54 dependent transcriptional regulator (VIMSS)

CircVis
Functional Annotations (10)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0359
(Mouseover regulator name to see its description)

GSU0359 is regulated by 18 influences and regulates 27 modules.
Regulators for GSU0359 (18)
Regulator Module Operator
GSU0175 122 tf
GSU0300 122 tf
GSU0359 122 tf
GSU0735 122 tf
GSU0776 122 tf
GSU1940 122 tf
GSU2506 122 tf
GSU2716 122 tf
GSU3087 122 tf
GSU3217 122 tf
GSU0187 257 tf
GSU0359 257 tf
GSU0655 257 tf
GSU1495 257 tf
GSU1626 257 tf
GSU2581 257 tf
GSU3363 257 tf
GSU3370 257 tf

Warning: GSU0359 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
2404 2.90e+03 AAAtaTaTgAAcaaA
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2405 1.90e+04 AgacAaAacccaaGGAGgaaCTcC
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2674 1.40e+03 GcccCtgcaCCGgcCac
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2675 2.90e+04 ATActctATACacT
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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 GSU0359

GSU0359 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
sensory_box tigr/ tigrfam
Module neighborhood information for GSU0359

GSU0359 has total of 50 gene neighbors in modules 122, 257
Gene neighbors (50)
Gene Common Name Description Module membership
GSU0040 GSU0040 conserved hypothetical protein (VIMSS) 137, 257
GSU0190 GSU0190 hypothetical protein (VIMSS) 109, 257
GSU0222 GSU0222 cytochrome c oxidase, subunit II (VIMSS) 99, 257
GSU0223 GSU0223 protoheme IX farnesyl transferase, putative (VIMSS) 257, 300
GSU0359 GSU0359 sensory box protein/sigma-54 dependent transcriptional regulator (VIMSS) 122, 257
GSU0385 GSU0385 NADH dehydrogenase subunit, putative (VIMSS) 243, 257
GSU0528 GSU0528 nitroreductase family protein (NCBI) 122, 281
GSU0530 GSU0530 HIT family protein (VIMSS) 122, 281
GSU0549 GSU0549 conserved domain protein (NCBI) 122, 287
GSU0749 GSU0749 hypothetical protein (VIMSS) 78, 122
GSU0752 GSU0752 transporter, putative (VIMSS) 216, 257
GSU0756 GSU0756 methyl-accepting chemotaxis protein (VIMSS) 122, 317
GSU0768 GSU0768 AzlC family protein (VIMSS) 99, 122
GSU0771 GSU0771 alcohol dehydrogenase, zinc-containing (VIMSS) 16, 257
GSU0773 GSU0773 multidrug resistance protein, putative (VIMSS) 16, 257
GSU0774 GSU0774 iron-sulfur cluster-binding protein (VIMSS) 109, 257
GSU0775 GSU0775 sensor histidine kinase (VIMSS) 122, 184
GSU0819 GSU0819 conserved hypothetical protein (VIMSS) 122, 337
GSU0901 fragment conserved domain protein (NCBI) 257, 287
GSU1052 GSU1052 hydrolase, alpha/beta fold family (VIMSS) 122, 153
GSU1053 GSU1053 sensory box protein (VIMSS) 122, 126
GSU1272 pyrC dihydroorotase, multifunctional complex type (NCBI) 122, 281
GSU1305 gdhA Glu/Leu/Phe/Val dehydrogenase family protein (NCBI) 32, 122
GSU2001 mutL DNA mismatch repair protein MutL (NCBI) 122, 281
GSU2314 GSU2314 sensory box histidine kinase/response regulator (VIMSS) 155, 257
GSU2316 GSU2316 mechanosensitive ion channel family protein (NCBI) 140, 257
GSU2352 GSU2352 sodium/solute symporter family protein (NCBI) 32, 122
GSU2411 GSU2411 conserved hypothetical protein TIGR00104 (VIMSS) 122, 281
GSU2432 GSU2432 cytochrome c family protein (VIMSS) 13, 122
GSU2481 kdpB potassium-transporting ATPase, B subunit (NCBI) 96, 257
GSU2484 kdpE DNA-binding response regulator KdpE (NCBI) 96, 257
GSU2486 GSU2486 conserved hypothetical protein (VIMSS) 257, 311
GSU2557 GSU2557 polysaccharide deacetylase family protein (NCBI) 122, 135
GSU2574 GSU2574 response regulator (VIMSS) 122, 287
GSU2630 GSU2630 serine/threonine protein phosphatase, putative (VIMSS) 155, 257
GSU2768 GSU2768 hypothetical protein (VIMSS) 122, 135
GSU2881 GSU2881 hypothetical protein (VIMSS) 122, 142
GSU2902 GSU2902 TPR domain protein (VIMSS) 109, 257
GSU2904 GSU2904 hypothetical protein (NCBI) 186, 257
GSU2905 GSU2905 radical SAM domain protein (NCBI) 166, 257
GSU3016 GSU3016 hypothetical protein (VIMSS) 122, 135
GSU3018 GSU3018 conserved hypothetical protein (VIMSS) 27, 257
GSU3120 GSU3120 conserved hypothetical protein (VIMSS) 122, 135
GSU3122 GSU3122 metallo-beta-lactamase family protein (NCBI) 137, 257
GSU3126 GSU3126 oxidoreductase, aldo/keto reductase family (VIMSS) 137, 257
GSU3311 GSU3311 hypothetical protein (VIMSS) 166, 257
GSU3363 GSU3363 sigma-54 dependent transcriptional regulator, Fis family (VIMSS) 109, 257
GSU3398 GSU3398 metal ion efflux outer membrane protein family protein, putative (VIMSS) 122, 337
GSU3399 GSU3399 efflux transporter, RND family, MFP subunit (NCBI) 122, 337
GSU4009 GSU4009 None 70, 122
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 GSU0359
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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