Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3018

radical SAM domain-containing protein

CircVis
Functional Annotations (4)
Function System
Predicted Fe-S oxidoreductases cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3018
(Mouseover regulator name to see its description)

DVU3018 is regulated by 17 influences and regulates 0 modules.
Regulators for DVU3018 (17)
Regulator Module Operator
DVU0309
DVU3220
184 combiner
DVU1584
DVU0269
184 combiner
DVU2114 184 tf
DVU2547
DVU0309
184 combiner
DVU2547
DVU2989
184 combiner
DVU2802
DVU0110
184 combiner
DVU3255
DVU3186
184 combiner
DVU0309
DVU0621
125 combiner
DVU0309
DVU2989
125 combiner
DVU1584
DVU0269
125 combiner
DVU2423
DVU1419
125 combiner
DVU2547
DVU0539
125 combiner
DVU2547
DVU2989
125 combiner
DVU2802
DVU0539
125 combiner
DVU3255
DVU1156
125 combiner
DVU3255
DVU1584
125 combiner
DVU3255
DVU3186
125 combiner

Warning: DVU3018 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.
Click on the RegPredict links to explore the motif in RegPredict.

Motif Table (4)
Motif Id e-value Consensus Motif Logo RegPredict
241 2.10e+01 cTGcCGGcatccTGcCCgCatCa
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RegPredict
242 4.90e+00 TC.gcACa.TGcaatagaAagGg
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RegPredict
351 2.20e+00 catGGaacgttcaTTGCtt
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RegPredict
352 4.10e+03 AACACaaTGGAATAaAA
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RegPredict
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 DVU3018

DVU3018 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted Fe-S oxidoreductases cog/ cog
catalytic activity go/ molecular_function
metabolic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
Module neighborhood information for DVU3018

DVU3018 has total of 31 gene neighbors in modules 125, 184
Gene neighbors (31)
Gene Common Name Description Module membership
DVU0044 fliP flagellar biosynthesis protein FliP 184, 286
DVU0046 fliN flagellar motor switch protein FliN 115, 184
DVU0047 flagellar protein FliL 184, 298
DVU0310 fliI flagellum-specific ATP synthase FliI 125, 184
DVU0311 flagellar assembly protein FliH 125, 184
DVU0312 fliG flagellar motor switch protein FliG 125, 184
DVU0313 fliF flagellar M-ring protein FliF 125, 184
DVU0314 fliE flagellar basal body component FliE 125, 184
DVU0315 flgC flagellar basal-body rod protein FlgC 125, 184
DVU0409 hypothetical protein DVU0409 22, 184
DVU0512 flagellar basal-body rod protein 125, 184
DVU0513 flgG flagellar basal body rod protein FlgG 125, 184
DVU0515 flgH flagellar basal body L-ring protein 125, 184
DVU0516 flgI flagellar basal body P-ring protein 125, 184
DVU0517 M24/M37 family peptidase 125, 184
DVU0519 flagellar hook-associated protein FlgK 125, 184
DVU0520 flagellar hook-associated protein FlgL 22, 184
DVU0521 csrA carbon storage regulator 184, 249
DVU0522 flagellar assembly protein FliW 184, 208
DVU0858 lipoprotein 82, 184
DVU0862 bifunctional flagellar protein FliS/hypothetical protein 22, 184
DVU0863 flagellar hook-associated protein 2 22, 184
DVU0913 hypothetical protein DVU0913 125, 184
DVU2211 hypothetical protein DVU2211 103, 184
DVU2232 hypothetical protein DVU2232 125, 184
DVU3001 hypothetical protein DVU3001 22, 184
DVU3003 radical SAM domain-containing protein 125, 184
DVU3004 radical SAM domain-containing protein 22, 125
DVU3018 radical SAM domain-containing protein 125, 184
DVU3019 radical SAM/B12 binding domain-containing protein 125, 184
DVU3020 hypothetical protein DVU3020 125, 184
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 DVU3018
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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