Organism : Geobacter sulfurreducens | Module List :
GSU0082 RluD

ribosomal large subunit pseudouridine synthase D (NCBI)

CircVis
Functional Annotations (6)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridylate synthase activity go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU0082
(Mouseover regulator name to see its description)

GSU0082 is regulated by 21 influences and regulates 0 modules.
Regulators for GSU0082 RluD (21)
Regulator Module Operator
GSU0031 326 tf
GSU0372 326 tf
GSU1250 326 tf
GSU1653 326 tf
GSU2524 326 tf
GSU2540 326 tf
GSU2753 326 tf
GSU2964 326 tf
GSU3087 326 tf
GSU3396 326 tf
GSU3457 326 tf
GSU0018 261 tf
GSU0581 261 tf
GSU1522 261 tf
GSU1525 261 tf
GSU1626 261 tf
GSU1687 261 tf
GSU1727 261 tf
GSU1934 261 tf
GSU2524 261 tf
GSU2581 261 tf

Warning: GSU0082 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
2682 3.90e+02 gtTtTcCC
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2683 1.20e+03 AAaa.Gtt.aaacaAtg.aA
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2808 5.70e+00 aaagt.GAacGgT.TtacCTtTtG
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2809 4.70e+02 CTTGAC
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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 GSU0082

GSU0082 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridylate synthase activity go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
Module neighborhood information for GSU0082

GSU0082 has total of 33 gene neighbors in modules 261, 326
Gene neighbors (33)
Gene Common Name Description Module membership
GSU0082 RluD ribosomal large subunit pseudouridine synthase D (NCBI) 261, 326
GSU0124 GSU0124 competence protein F, putative (VIMSS) 59, 261
GSU0125 GSU0125 conserved hypothetical protein (VIMSS) 218, 261
GSU0200 iorA isoquinoline 1-oxidoreductase, alpha subunit (NCBI) 188, 261
GSU0201 iorB isoquinoline 1-oxidoreductase, beta subunit (NCBI) 261, 288
GSU0728 GSU0728 conserved hypothetical protein (VIMSS) 178, 261
GSU1059 sucD succinyl-CoA synthase, alpha subunit (NCBI) 100, 326
GSU1161 GSU1161 efflux transporter, RND family, MFP subunit (NCBI) 310, 326
GSU1614 GSU1614 CoA-binding protein (VIMSS) 20, 326
GSU2325 GSU2325 cation-transport ATPase, E1-E2 family (VIMSS) 27, 261
GSU2446 lpdA-1 2-oxoglutarate dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI) 167, 261
GSU2656 aceF pyruvate dehydrogenase complex E2 component, dihydrolipoamide acetyltransferase (NCBI) 261, 339
GSU2728 GSU2728 hypothetical protein (VIMSS) 261, 339
GSU2788 GSU2788 conserved hypothetical protein (NCBI) 128, 326
GSU2922 GSU2922 hypothetical protein (VIMSS) 38, 261
GSU3130 GSU3130 lipoprotein, putative (VIMSS) 100, 326
GSU3138 GSU3138 sensor histidine kinase/response regulator (VIMSS) 100, 326
GSU3151 GSU3151 conserved hypothetical protein (VIMSS) 165, 261
GSU3192 GSU3192 heat shock protein, Hsp20 family (NCBI) 104, 326
GSU3194 thiL thiamine monophosphate kinase (NCBI) 128, 326
GSU3195 GSU3195 chemotaxis protein methyltransferase CheR,putative (VIMSS) 104, 326
GSU3196 GSU3196 methyl-accepting chemotaxis protein (VIMSS) 246, 326
GSU3197 GSU3197 purine-binding chemotaxis protein CheW, putative (VIMSS) 246, 326
GSU3198 cheY-7 chemotaxis protein CheY (NCBI) 189, 326
GSU3199 cheA-3 chemotaxis protein CheA (NCBI) 246, 326
GSU3200 GSU3200 chemotaxis protein, CheC family (NCBI) 100, 326
GSU3201 GSU3201 chemotaxis protein CheD, putative (VIMSS) 104, 326
GSU3202 GSU3202 hypothetical protein (VIMSS) 189, 326
GSU3350 pleD sensor histidine kinase/GGDEF domain protein (NCBI) 182, 261
GSU3356 GSU3356 GGDEF domain/HAMP domain protein (NCBI) 246, 261
GSU3359 GSU3359 conserved hypothetical protein (VIMSS) 261, 339
GSU3425 GSU3425 hypothetical protein (VIMSS) 261, 312
GSU3442 GSU3442 conserved hypothetical protein (VIMSS) 167, 326
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 GSU0082
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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