Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3255

CopG family transcriptional regulator

CircVis
Functional Annotations (1)
Function System
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3255
(Mouseover regulator name to see its description)

DVU3255 is regulated by 29 influences and regulates 69 modules.
Regulators for DVU3255 (29)
Regulator Module Operator
DVU0916 48 tf
DVU1517 48 tf
DVU1967
DVU0539
48 combiner
DVU2114 48 tf
DVU2557 48 tf
DVU2557
DVU0946
48 combiner
DVU2690 48 tf
DVU2788
DVU0946
48 combiner
DVU2832
DVU1745
48 combiner
DVU2909
DVU0230
48 combiner
DVUA0143
DVU3066
48 combiner
DVU1156 300 tf
DVU1572
DVU0946
300 combiner
DVU1572
DVU2036
300 combiner
DVU1584
DVU0110
300 combiner
DVU1584
DVU0946
300 combiner
DVU1584
DVU3023
300 combiner
DVU1754 300 tf
DVU2036
DVU2582
300 combiner
DVU2036
DVU3186
300 combiner
DVU2086 300 tf
DVU2086
DVU2588
300 combiner
DVU2086
DVU2832
300 combiner
DVU3023 300 tf
DVU3142 300 tf
DVU3167
DVU0682
300 combiner
DVU3167
DVU1584
300 combiner
DVU3186 300 tf
DVUA0057 300 tf

Warning: DVU3255 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
95 1.70e+02 CtGAAAAG
Loader icon
RegPredict
96 1.70e+02 cGGacAtGaTg
Loader icon
RegPredict
575 4.00e+01 TcAtttT.TTT
Loader icon
RegPredict
576 1.20e+03 AGGaTGTg
Loader icon
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 DVU3255

DVU3255 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for DVU3255

DVU3255 has total of 36 gene neighbors in modules 48, 300
Gene neighbors (36)
Gene Common Name Description Module membership
DVU0079 ZIP zinc transporter family protein 48, 135
DVU0106 glnP glutamine ABC transporter permease 88, 300
DVU0128 hypothetical protein DVU0128 48, 268
DVU0280 glycosyl transferase group 1 family protein 98, 300
DVU0327 exopolysaccharide biosynthesis protein 48, 327
DVU0413 TrkH family potassium uptake protein 48, 117
DVU0441 ade adenine deaminase 14, 48
DVU0511 hypothetical protein DVU0511 10, 300
DVU0612 STAS domain-containing protein 48, 117
DVU0788 mreC rod shape-determining protein MreC 300, 336
DVU1019 hypothetical protein DVU1019 48, 187
DVU1050 ccmF cytochrome c-type biogenesis protein CcmF 52, 300
DVU1076 hypothetical protein DVU1076 237, 300
DVU1242 vacJ lipoprotein 48, 164
DVU1246 hypothetical protein DVU1246 163, 300
DVU1458 chemotaxis protein CheZ 48, 268
DVU1590 radA DNA repair protein RadA 48, 268
DVU1611 molybdopterin oxidoreductase domain-containing protein 48, 327
DVU1650 hypothetical protein DVU1650 300, 303
DVU1813 hypothetical protein DVU1813 48, 241
DVU1814 cytochrome c oxidase subunit III 48, 241
DVU1831 None 88, 300
DVU1840 glycoprotease family metalloendopeptidase 237, 300
DVU1843 hypothetical protein DVU1843 163, 300
DVU2243 glgB glycogen branching enzyme 48, 268
DVU2371 N-acetylmuramoyl-L-alanine amidase 163, 300
DVU2375 lipoprotein releasing system, permease 300, 336
DVU2409 solute-binding family 3 protein 48, 187
DVU2484 cytochrome c family protein 48, 268
DVU2485 hypothetical protein DVU2485 48, 268
DVU2762 hypothetical protein DVU2762 48, 268
DVU2787 hypothetical protein DVU2787 48, 181
DVU3161 ABC transporter ATP-binding protein 23, 300
DVU3255 CopG family transcriptional regulator 48, 300
DVU3261 frdC fumarate reductase, cytochrome subunit B 48, 303
DVU3375 cell division ATP-binding protein FtsE 48, 343
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 DVU3255
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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