Organism : Geobacter sulfurreducens | Module List :
GSU1692 nusB

N utilization substance protein B (NCBI)

CircVis
Functional Annotations (6)
Function System
Transcription termination factor cog/ cog
transcription termination factor activity go/ molecular_function
RNA binding go/ molecular_function
transcription termination, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
nusB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU1692
(Mouseover regulator name to see its description)

GSU1692 is regulated by 21 influences and regulates 32 modules.
Regulators for GSU1692 nusB (21)
Regulator Module Operator
GSU0732 80 tf
GSU1483 80 tf
GSU1692 80 tf
GSU1727 80 tf
GSU1992 80 tf
GSU2262 80 tf
GSU2581 80 tf
GSU2666 80 tf
GSU3053 80 tf
GSU3087 80 tf
GSU0732 263 tf
GSU1483 263 tf
GSU1525 263 tf
GSU1692 263 tf
GSU1727 263 tf
GSU2237 263 tf
GSU2581 263 tf
GSU2817 263 tf
GSU2831 263 tf
GSU3045 263 tf
GSU3087 263 tf

Warning: GSU1692 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
2320 2.00e+02 AatTcaCCaA
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2321 3.80e+03 aCCcTTGACagacCA
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2686 3.30e+00 tcg.AaaAcccgtCaatTctaCca
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2687 4.00e+03 Tt.tTcCTTGAcgt
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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 GSU1692

GSU1692 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Transcription termination factor cog/ cog
transcription termination factor activity go/ molecular_function
RNA binding go/ molecular_function
transcription termination, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
nusB tigr/ tigrfam
Module neighborhood information for GSU1692

GSU1692 has total of 36 gene neighbors in modules 80, 263
Gene neighbors (36)
Gene Common Name Description Module membership
GSU0162 aspC aromatic aminotransferase, putative (NCBI) 39, 263
GSU0197 GSU0197 oxidoreductase, short chain dehydrogenase/reductase family (VIMSS) 80, 169
GSU0327 hofF general secretion pathway protein F (NCBI) 28, 263
GSU0488 trxB thioredoxin reductase (NCBI) 80, 263
GSU0521 GSU0521 methyltransferase, putative (VIMSS) 5, 263
GSU0531 dapF diaminopimelate epimerase (NCBI) 80, 276
GSU1122 GSU1122 HD domain protein (NCBI) 52, 80
GSU1139 tyrS tyrosyl-tRNA synthetase (NCBI) 263, 316
GSU1150 GSU1150 oxidative cyclase-related protein (VIMSS) 80, 263
GSU1166 GSU1166 TPR domain protein (NCBI) 80, 111
GSU1193 GSU1193 ketose-bisphosphate aldolase family protein (VIMSS) 39, 80
GSU1211 GSU1211 conserved hypothetical protein (VIMSS) 80, 215
GSU1224 GSU1224 TPR domain protein (VIMSS) 255, 263
GSU1328 GSU1328 conserved hypothetical protein (VIMSS) 80, 196
GSU1463 aspS aspartyl-tRNA synthetase (NCBI) 215, 263
GSU1644 GSU1644 ABC transporter, ATP-binding protein (VIMSS) 80, 162
GSU1692 nusB N utilization substance protein B (NCBI) 80, 263
GSU1693 hom homoserine dehydrogenase (NCBI) 52, 263
GSU1827 nadB L-aspartate oxidase (NCBI) 80, 263
GSU1830 GSU1830 conserved hypothetical protein (VIMSS) 80, 205
GSU1833 trpS tryptophanyl-tRNA synthetase (NCBI) 80, 263
GSU1880 metK S-adenosylmethionine synthetase (RefSeq) 137, 263
GSU1884 GSU1884 conserved hypothetical protein (VIMSS) 136, 263
GSU1885 hprK HPr(Ser) kinase/phosphatase (NCBI) 263, 313
GSU1894 kdsA 2-dehydro-3-deoxyphosphooctonate aldolase (NCBI) 5, 263
GSU2270 GSU2270 ABC transporter, permease protein (VIMSS) 263, 277
GSU2271 lysS lysyl-tRNA synthetase (NCBI) 28, 263
GSU2272 GSU2272 lipoprotein, putative (VIMSS) 80, 126
GSU2333 GSU2333 membrane protein, putative (VIMSS) 80, 111
GSU2381 trpD anthranilate phosphoribosyltransferase (NCBI) 80, 196
GSU2513 GSU2513 cytochrome c family protein (VIMSS) 80, 197
GSU2970 GSU2970 conserved hypothetical protein (VIMSS) 80, 137
GSU3134 GSU3134 hypothetical protein (VIMSS) 80, 225
GSU3285 hemC porphobilinogen deaminase (NCBI) 44, 263
GSU3392 GSU3392 branched-chain amino acid ABC transporter, ATP-binding protein (NCBI) 80, 136
GSU3394 GSU3394 branched-chain amino acid ABC transporter, permease protein (NCBI) 80, 176
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 GSU1692
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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