Organism : Geobacter sulfurreducens | Module List :
GSU0732

nucleoside diphosphate kinase regulator protein, putative (VIMSS)

CircVis
Functional Annotations (4)
Function System
Transcription elongation factor cog/ cog
DNA binding go/ molecular_function
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0732
(Mouseover regulator name to see its description)

GSU0732 is regulated by 19 influences and regulates 38 modules.
Regulators for GSU0732 (19)
Regulator Module Operator
GSU0031 39 tf
GSU0581 39 tf
GSU0732 39 tf
GSU1201 39 tf
GSU1218 39 tf
GSU1270 39 tf
GSU1320 39 tf
GSU1692 39 tf
GSU1727 39 tf
GSU2964 39 tf
GSU0732 74 tf
GSU1201 74 tf
GSU1218 74 tf
GSU1525 74 tf
GSU1626 74 tf
GSU1692 74 tf
GSU1727 74 tf
GSU2520 74 tf
GSU2523 74 tf

Warning: GSU0732 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
2238 5.50e+03 TaAtACAAC
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2239 5.20e+03 GAtCGGCagcA
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2308 4.80e+02 AGGGGG
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2309 1.50e+03 atActttaTcGcaa
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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 GSU0732

GSU0732 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcription elongation factor cog/ cog
DNA binding go/ molecular_function
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for GSU0732

GSU0732 has total of 32 gene neighbors in modules 39, 74
Gene neighbors (32)
Gene Common Name Description Module membership
GSU0003 gyrB DNA gyrase, B subunit (NCBI) 31, 39
GSU0004 gyrA DNA gyrase, A subunit (NCBI) 74, 192
GSU0010 GSU0010 sensory box histidine kinase/response regulator (VIMSS) 39, 295
GSU0119 GSU0119 glyoxalase family protein (NCBI) 74, 111
GSU0162 aspC aromatic aminotransferase, putative (NCBI) 39, 263
GSU0215 folD-1 folD bifunctional protein (NCBI) 39, 106
GSU0732 GSU0732 nucleoside diphosphate kinase regulator protein, putative (VIMSS) 39, 74
GSU1076 ruvA Holliday junction DNA helicase RuvA (NCBI) 39, 174
GSU1193 GSU1193 ketose-bisphosphate aldolase family protein (VIMSS) 39, 80
GSU1200 rpsA ribosomal protein S1 (NCBI) 74, 192
GSU1271 pyrB aspartate carbamoyltransferase (NCBI) 39, 295
GSU1273 carA carbamoyl-phosphate synthase, small subunit (NCBI) 39, 212
GSU1525 rpoD RNA polymerase sigma-70 factor family (NCBI) 74, 192
GSU1530 hisG-1 ATP phosphoribosyltransferase (NCBI) 39, 52
GSU1698 GSU1698 TPR domain protein (VIMSS) 39, 276
GSU1732 GSU1732 branched-chain amino acid ABC transporter, permease protein (NCBI) 74, 255
GSU1735 GSU1735 branched-chain amino acid ABC transporter, periplasmic amino acid-binding protein, putative (NCBI) 74, 255
GSU1736 GSU1736 ACT domain protein (VIMSS) 74, 255
GSU1737 GSU1737 phenylacetate-CoA ligase (NCBI) 74, 255
GSU1739 GSU1739 indolepyruvate ferredoxin oxidoreductase, alpha subunit (VIMSS) 74, 255
GSU1754 kamA L-lysine 2,3-aminomutase (NCBI) 74, 139
GSU1908 GSU1908 phosphatidylserine decarboxylase, putative (NCBI) 39, 106
GSU1909 ilvC ketol-acid reductoisomerase (NCBI) 39, 74
GSU1912 ilvD dihydroxy-acid dehydratase (NCBI) 39, 276
GSU2046 GSU2046 response regulator (NCBI) 39, 204
GSU2366 rfbB dTDP-glucose 4,6-dehydratase (NCBI) 74, 328
GSU2466 GSU2466 hypothetical protein (VIMSS) 39, 296
GSU2558 GSU2558 conserved domain protein (VIMSS) 39, 174
GSU2601 GSU2601 TPR domain/SEC-C motif domain protein (NCBI) 39, 106
GSU2604 lytB penicillin tolerance protein LytB (NCBI) 31, 74
GSU3391 GSU3391 branched-chain amino acid ABC transporter, ATP-binding protein (NCBI) 31, 74
GSU3393 GSU3393 branched-chain amino acid ABC transporter, permease protein (NCBI) 74, 192
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 GSU0732
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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