Organism : Geobacter sulfurreducens | Module List :
GSU2926

(R)-2-hydroxyglutaryl-CoA dehydratase activator, putative (VIMSS)

CircVis
Functional Annotations (3)
Function System
Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) cog/ cog
carbohydrate metabolic process go/ biological_process
CoA_E_activ tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for GSU2926
(Mouseover regulator name to see its description)

GSU2926 is regulated by 21 influences and regulates 13 modules.
Regulators for GSU2926 (21)
Regulator Module Operator
GSU0018 38 tf
GSU0655 38 tf
GSU1201 38 tf
GSU1419 38 tf
GSU1934 38 tf
GSU2185 38 tf
GSU2523 38 tf
GSU2625 38 tf
GSU2926 38 tf
GSU2945 38 tf
GSU0284 203 tf
GSU0655 203 tf
GSU0963 203 tf
GSU2185 203 tf
GSU2523 203 tf
GSU2571 203 tf
GSU2587 203 tf
GSU2670 203 tf
GSU2926 203 tf
GSU2945 203 tf
GSU3206 203 tf

Warning: GSU2926 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
2236 1.20e+00 ATaCATtattaAc.GaaGc
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2237 1.20e+01 aAG..atatTaccTtGtCatgccA
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2566 1.30e-02 tgTaAaaacTg.AaATAcT
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2567 1.10e+01 aaAtGgcttg.CaaGgtAA
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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 GSU2926

GSU2926 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Activator of 2-hydroxyglutaryl-CoA dehydratase (HSP70-class ATPase domain) cog/ cog
carbohydrate metabolic process go/ biological_process
CoA_E_activ tigr/ tigrfam
Module neighborhood information for GSU2926

GSU2926 has total of 44 gene neighbors in modules 38, 203
Gene neighbors (44)
Gene Common Name Description Module membership
GSU0131 GSU0131 conserved hypothetical protein (VIMSS) 172, 203
GSU0134 GSU0134 metallo-beta-lactamase family protein (NCBI) 38, 59
GSU0216 GSU0216 conserved hypothetical protein (VIMSS) 38, 241
GSU0283 GSU0283 sensor histidine kinase (VIMSS) 99, 203
GSU0284 dksA dnaK suppressor protein (NCBI) 203, 273
GSU0593 GSU0593 conserved domain protein (NCBI) 38, 241
GSU0594 GSU0594 cytochrome c family protein (NCBI) 38, 241
GSU1027 GSU1027 glycosyl hydrolase, family 10 (VIMSS) 63, 203
GSU1028 GSU1028 peptidylarginine deiminase-related protein (NCBI) 63, 203
GSU1125 GSU1125 hypothetical protein (VIMSS) 77, 203
GSU1337 GSU1337 hypothetical protein (VIMSS) 203, 321
GSU1400 GSU1400 None 38, 92
GSU1452 GSU1452 RNA methyltransferase, TrmA family (VIMSS) 38, 203
GSU1685 GSU1685 HD domain protein (NCBI) 21, 38
GSU1699 GSU1699 TonB-dependent receptor, putative (VIMSS) 38, 321
GSU1857 GSU1857 hypothetical protein (VIMSS) 53, 203
GSU1937 GSU1937 GGDEF domain/HAMP domain protein (NCBI) 203, 321
GSU1939 GSU1939 GAF domain/His Kinase A domain/HD domain protein (NCBI) 114, 203
GSU1944 GSU1944 hypothetical protein (VIMSS) 38, 241
GSU2184 GSU2184 polyA polymerase family protein (NCBI) 38, 321
GSU2196 GSU2196 hydrolase, putative (VIMSS) 203, 321
GSU2197 GSU2197 conserved hypothetical protein (VIMSS) 203, 218
GSU2198 miaB tRNA-i(6)A37 modification enzyme MiaB (NCBI) 203, 321
GSU2301 GSU2301 hypothetical protein (VIMSS) 201, 203
GSU2920 GSU2920 hypothetical protein (VIMSS) 38, 321
GSU2921 metH 5-methyltetrahydrofolate-homocysteine methyltransferase, truncation (NCBI) 38, 203
GSU2922 GSU2922 hypothetical protein (VIMSS) 38, 261
GSU2923 murI glutamate racemase (NCBI) 38, 203
GSU2924 GSU2924 hypothetical protein (VIMSS) 38, 203
GSU2925 GSU2925 conserved hypothetical protein (VIMSS) 38, 203
GSU2926 GSU2926 (R)-2-hydroxyglutaryl-CoA dehydratase activator, putative (VIMSS) 38, 203
GSU3012 GSU3012 hypothetical protein (VIMSS) 38, 157
GSU3096 hisA phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (NCBI) 172, 203
GSU3098 hisB imidazoleglycerol-phosphate dehydratase (NCBI) 203, 315
GSU3099 hisC histidinol-phosphate aminotransferase (NCBI) 38, 203
GSU3100 hisD histidinol dehydrogenase (NCBI) 71, 203
GSU3101 hisG-2 ATP phosphoribosyltransferase (NCBI) 172, 203
GSU3102 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase (NCBI) 172, 203
GSU3269 GSU3269 None 38, 107
GSU3280 GSU3280 thioredoxin-related protein (NCBI) 44, 203
GSU3295 GSU3295 conserved hypothetical protein (VIMSS) 38, 321
GSU3296 GSU3296 glycolate oxidase subunit GlcD, putative (VIMSS) 38, 321
GSU3297 GSU3297 iron-sulfur cluster-binding protein (NCBI) 38, 321
GSU3325 uvrA excinuclease ABC, A subunit (NCBI) 38, 266
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 GSU2926
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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