Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1628 rpoN

RNA polymerase sigma-54 factor

CircVis
Functional Annotations (12)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoN_sigma tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1628
(Mouseover regulator name to see its description)

DVU1628 is regulated by 33 influences and regulates 28 modules.
Regulators for DVU1628 rpoN (33)
Regulator Module Operator
DVU0110 110 tf
DVU0813 110 tf
DVU0854 110 tf
DVU1340 110 tf
DVU1561
DVU0619
110 combiner
DVU1584 110 tf
DVU1788 110 tf
DVU2086 110 tf
DVU2086
DVU0744
110 combiner
DVU2359 110 tf
DVU2423 110 tf
DVU2547 110 tf
DVU2547
DVU2359
110 combiner
DVU2582 110 tf
DVU2819 110 tf
DVU3095 110 tf
DVU3111 110 tf
DVU3167 110 tf
DVU3220 110 tf
DVU3381 110 tf
DVU0230 90 tf
DVU0277 90 tf
DVU0596 90 tf
DVU0813 90 tf
DVU1690 90 tf
DVU1788 90 tf
DVU2086 90 tf
DVU2359 90 tf
DVU2359
DVU0525
90 combiner
DVU2547 90 tf
DVU3111 90 tf
DVU3167 90 tf
DVU3381 90 tf

Warning: DVU1628 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
177 2.00e-01 gtataacacta.aTcaagaaa..A
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RegPredict
178 1.40e+03 cAataGatgac.Atgaaattc
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RegPredict
211 3.10e-03 gatGtcTttttTtccAatt.A
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RegPredict
212 6.60e+01 gCAttatatgac.AtGaaCatc
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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 DVU1628

DVU1628 is enriched for 12 functions in 3 categories.
Enrichment Table (12)
Function System
DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
DNA-directed RNA polymerase activity go/ molecular_function
DNA-directed RNA polymerase I activity go/ molecular_function
DNA-directed RNA polymerase II activity go/ molecular_function
DNA-directed RNA polymerase III activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
Two-component system kegg/ kegg pathway
RNA polymerase kegg/ kegg pathway
rpoN_sigma tigr/ tigrfam
Module neighborhood information for DVU1628

DVU1628 has total of 41 gene neighbors in modules 90, 110
Gene neighbors (41)
Gene Common Name Description Module membership
DVU0223 hypothetical protein DVU0223 90, 156
DVU0298 hypothetical protein DVU0298 110, 120
DVU0421 agmatinase 110, 120
DVU0526 drug resistance transporter 90, 120
DVU0727 hypothetical protein DVU0727 90, 110
DVU0728 hypothetical protein DVU0728 90, 110
DVU0756 hypothetical protein 90, 110
DVU0801 uvrC excinuclease ABC subunit C 57, 110
DVU0866 dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase 110, 226
DVU0955 alr alanine racemase 110, 225
DVU0985 hypothetical protein DVU0985 57, 110
DVU1013 TolC family type I secretion outer membrane protein 4, 110
DVU1151 hypothetical protein DVU1151 90, 110
DVU1379 hypothetical protein DVU1379 70, 90
DVU1492 None 90, 156
DVU1554 radical SAM domain-containing protein 110, 242
DVU1628 rpoN RNA polymerase sigma-54 factor 90, 110
DVU1629 yfiA ribosomal subunit interface protein 4, 90
DVU1630 PTS system transporter subunit IIA 90, 330
DVU1644 permease 110, 226
DVU1645 ArsR family transcriptional regulator 110, 226
DVU1710 hypothetical protein DVU1710 90, 210
DVU1729 killer protein 13, 90
DVU1730 DNA-binding protein 90, 289
DVU1855 integrase, truncation 90, 227
DVU2001 None 90, 220
DVU2282 hypothetical protein DVU2282 110, 173
DVU2309 methyl-accepting chemotaxis protein 90, 110
DVU2362 thiE thiamine-phosphate pyrophosphorylase 66, 110
DVU2423 transcriptional regulator 90, 289
DVU2439 RND family efflux transporter MFP subunit 4, 110
DVU2548 acpD ACP phosphodiesterase 110, 194
DVU2614 hypothetical protein DVU2614 41, 90
DVU2662 hypothetical protein DVU2662 110, 226
DVU2845 HIT family protein 90, 309
DVU2846 hypothetical protein DVU2846 90, 335
DVU3079 glyoxalase family protein 110, 274
DVU3135 flavodoxin-like fold domain-containing protein 110, 274
DVU3136 nitroreductase family protein 110, 274
DVU3316 pyrD dihydroorotate dehydrogenase 4, 110
DVUA0089 hypothetical protein DVUA0089 90, 247
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 DVU1628
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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