Organism : Geobacter sulfurreducens | Module List :
GSU1053

sensory box protein (VIMSS)

CircVis
Functional Annotations (5)
Function System
FOG: PAS/PAC domain cog/ cog
two-component sensor activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1053
(Mouseover regulator name to see its description)

GSU1053 is regulated by 19 influences and regulates 0 modules.
Regulators for GSU1053 (19)
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
GSU0514 126 tf
GSU0551 126 tf
GSU0770 126 tf
GSU1687 126 tf
GSU1692 126 tf
GSU1989 126 tf
GSU1992 126 tf
GSU2262 126 tf
GSU3421 126 tf

Warning: GSU1053 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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2412 8.80e+02 CtCctGgGGggcCGg
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2413 5.60e+03 TctCcaTtTtTcCCT
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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 GSU1053

GSU1053 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
FOG: PAS/PAC domain cog/ cog
two-component sensor activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sensory_box tigr/ tigrfam
Module neighborhood information for GSU1053

GSU1053 has total of 56 gene neighbors in modules 122, 126
Gene neighbors (56)
Gene Common Name Description Module membership
GSU0087 GSU0087 heterodisulfide reductase, iron-sulfur binding subunit, putative (VIMSS) 126, 214
GSU0089 GSU0089 heterodisulfide reductase subunit (VIMSS) 126, 291
GSU0090 GSU0090 heterodisulfide reductase subunit (VIMSS) 126, 214
GSU0091 GSU0091 heterodisulfide reductase subunit (VIMSS) 126, 214
GSU0213 GSU0213 radical SAM domain protein (NCBI) 126, 323
GSU0226 GSU0226 L-lactate permease, putative (VIMSS) 126, 164
GSU0359 GSU0359 sensory box protein/sigma-54 dependent transcriptional regulator (VIMSS) 122, 257
GSU0526 GSU0526 conserved hypothetical protein (VIMSS) 126, 281
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
GSU0756 GSU0756 methyl-accepting chemotaxis protein (VIMSS) 122, 317
GSU0768 GSU0768 AzlC family protein (VIMSS) 99, 122
GSU0775 GSU0775 sensor histidine kinase (VIMSS) 122, 184
GSU0819 GSU0819 conserved hypothetical protein (VIMSS) 122, 337
GSU0825 GSU0825 pirin family protein (VIMSS) 126, 183
GSU0860 GSU0860 methylenetetrahydrofolate reductase family protein (VIMSS) 126, 144
GSU0862 folD-2 folD bifunctional protein (NCBI) 46, 126
GSU0903 GSU0903 None 126, 317
GSU1052 GSU1052 hydrolase, alpha/beta fold family (VIMSS) 122, 153
GSU1053 GSU1053 sensory box protein (VIMSS) 122, 126
GSU1124 coaBC phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase (NCBI) 126, 295
GSU1180 ftsH-1 cell division protein FtsH (NCBI) 112, 126
GSU1272 pyrC dihydroorotase, multifunctional complex type (NCBI) 122, 281
GSU1274 GSU1274 radical SAM domain protein (NCBI) 126, 208
GSU1298 GSU1298 methyl-accepting chemotaxis protein (VIMSS) 126, 183
GSU1305 gdhA Glu/Leu/Phe/Val dehydrogenase family protein (NCBI) 32, 122
GSU1377 GSU1377 3-hydroxybutyryl-CoA dehydratase (VIMSS) 11, 126
GSU1461 pyrF orotidine 5`-phosphate decarboxylase (NCBI) 126, 233
GSU1535 recD exodeoxyribonuclease V, alpha subunit (NCBI) 126, 336
GSU1710 GSU1710 None 126, 249
GSU2001 mutL DNA mismatch repair protein MutL (NCBI) 122, 281
GSU2047 GSU2047 conserved hypothetical protein (VIMSS) 26, 126
GSU2050 secA preprotein translocase, SecA subunit (NCBI) 91, 126
GSU2102 GSU2102 pyruvate formate-lyase-activating enzyme, putative (VIMSS) 126, 183
GSU2214 cheB-3 protein-glutamate methylesterase (NCBI) 126, 295
GSU2222 cheA-2 chemotaxis protein CheA (NCBI) 126, 222
GSU2272 GSU2272 lipoprotein, putative (VIMSS) 80, 126
GSU2352 GSU2352 sodium/solute symporter family protein (NCBI) 32, 122
GSU2375 GSU2375 None 126, 322
GSU2411 GSU2411 conserved hypothetical protein TIGR00104 (VIMSS) 122, 281
GSU2432 GSU2432 cytochrome c family protein (VIMSS) 13, 122
GSU2557 GSU2557 polysaccharide deacetylase family protein (NCBI) 122, 135
GSU2574 GSU2574 response regulator (VIMSS) 122, 287
GSU2768 GSU2768 hypothetical protein (VIMSS) 122, 135
GSU2879 leuB 3-isopropylmalate dehydrogenase (NCBI) 126, 233
GSU2881 GSU2881 hypothetical protein (VIMSS) 122, 142
GSU3016 GSU3016 hypothetical protein (VIMSS) 122, 135
GSU3062 GSU3062 radical SAM domain protein (NCBI) 42, 126
GSU3120 GSU3120 conserved hypothetical protein (VIMSS) 122, 135
GSU3260 GSU3260 phosphoserine aminotransferase, putative (VIMSS) 35, 126
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
GSU3421 GSU3421 transcriptional regulator, Crp/Fnr family (VIMSS) 126, 164
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 GSU1053
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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