Organism : Geobacter sulfurreducens | Module List :
GSU2868 nusG

transcription antitermination protein NusG (NCBI)

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

Cytoscape Web
Regulation information for GSU2868
(Mouseover regulator name to see its description)

GSU2868 is regulated by 16 influences and regulates 22 modules.
Regulators for GSU2868 nusG (16)
Regulator Module Operator
GSU1250 17 tf
GSU2113 17 tf
GSU2506 17 tf
GSU2625 17 tf
GSU2735 17 tf
GSU2787 17 tf
GSU2868 17 tf
GSU2915 17 tf
GSU0207 161 tf
GSU0359 161 tf
GSU1522 161 tf
GSU2041 161 tf
GSU2524 161 tf
GSU2831 161 tf
GSU2868 161 tf
GSU3387 161 tf

Warning: GSU2868 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
2194 8.30e-03 ttcatgTAAAt
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2195 3.90e+01 TgcAatAtTtAtTAaGtAgaT
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2482 7.70e+01 GTTCGAatCCcccCtcgCctaCCA
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2483 3.50e+03 GATTTG.A.ag.ataTaCAtA
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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 GSU2868

GSU2868 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Transcription antiterminator cog/ cog
transcription elongation regulator activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
nusG tigr/ tigrfam
Module neighborhood information for GSU2868

GSU2868 has total of 43 gene neighbors in modules 17, 161
Gene neighbors (43)
Gene Common Name Description Module membership
GSU0108 GSU0108 ATP synthase F0, B' subunit, putative (VIMSS) 154, 161
GSU0552 GSU0552 conserved domain protein (NCBI) 17, 129
GSU0561 GSU0561 conserved domain protein (NCBI) 17, 254
GSU0563 GSU0563 hypothetical protein (VIMSS) 17, 330
GSU0564 GSU0564 conserved hypothetical protein (VIMSS) 17, 330
GSU0662 rplY ribosoma protein L25 (NCBI) 154, 161
GSU0663 pth peptidyl-tRNA hydrolase (NCBI) 17, 161
GSU0664 ychF GTP binding protein YchF (NCBI) 35, 161
GSU0665 rpsF ribosomal protein S6 (NCBI) 58, 161
GSU1110 ndk nucleoside diphosphate kinase (NCBI) 154, 161
GSU1511 GSU1511 glycosyl transferase, group 1 family protein (NCBI) 17, 254
GSU1516 infC translation initiation factor IF-3 (NCBI) 154, 161
GSU1517 rpmI ribosomal protein L35 (NCBI) 75, 161
GSU1521 ihfA-1 integration host factor, alpha subunit (NCBI) 154, 161
GSU1522 GSU1522 transcriptional regulator, putative (VIMSS) 154, 161
GSU1590 GSU1590 DHH family/DHHA1 domain protein (NCBI) 17, 120
GSU1594 GSU1594 peptidase, M16 family (VIMSS) 17, 120
GSU1596 GSU1596 Sua5/YciO/YrdC/YwlC family protein (VIMSS) 17, 120
GSU1597 GSU1597 hypothetical protein (VIMSS) 17, 120
GSU1655 GSU1655 sensory box histidine kinase/response regulator (VIMSS) 17, 158
GSU1656 GSU1656 sensory box/response regulator (VIMSS) 17, 114
GSU1771 GSU1771 conserved domain protein (NCBI) 17, 170
GSU1781 GSU1781 hypothetical protein (VIMSS) 17, 18
GSU1782 GSU1782 conserved domain protein (NCBI) 17, 254
GSU1783 GSU1783 type IV pilus biogenesis protein PilB, putative (VIMSS) 17, 158
GSU1784 GSU1784 type IV pilus biogenesis protein PilC, putative (VIMSS) 17, 18
GSU1789 GSU1789 glycosyl transferase, group 2 family protein (VIMSS) 17, 33
GSU1791 clpX ATP-dependent Clp protease, ATP-binding subunit ClpX (VIMSS) 58, 161
GSU1792 clpP ATP-dependent Clp protease, proteolytic subunit ClpP (VIMSS) 161, 170
GSU1793 tig trigger factor (NCBI) 161, 170
GSU1850 GSU1850 hypothetical protein (VIMSS) 17, 42
GSU1851 GSU1851 glycosyl transferase, group 1 family protein (VIMSS) 17, 333
GSU1852 GSU1852 membrane protein, putative (VIMSS) 17, 274
GSU1895 pyrG CTP synthase (NCBI) 62, 161
GSU1919 pyrH uridylate kinase (NCBI) 154, 161
GSU2610 GSU2610 LysM domain protein (NCBI) 17, 330
GSU2694 GSU2694 hypothetical protein (VIMSS) 17, 147
GSU2864 rplL ribosomal protein L7/L12 (NCBI) 58, 161
GSU2865 rplJ ribosomal protein L10 (NCBI) 58, 161
GSU2868 nusG transcription antitermination protein NusG (NCBI) 17, 161
GSU2869 secE preprotein translocase, SecE subunit, putative (NCBI) 58, 161
GSU3079 GSU3079 hypothetical protein (VIMSS) 17, 207
GSU3093 rpsU-2 ribosomal protein S21 (NCBI) 56, 161
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 GSU2868
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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