Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2070

hypothetical protein

CircVis
Functional Annotations (3)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
binding go/ molecular_function
tol_pal_ybgF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2070
(Mouseover regulator name to see its description)

DVU2070 is regulated by 18 influences and regulates 0 modules.
Regulators for DVU2070 (18)
Regulator Module Operator
DVU0525 217 tf
DVU0653 217 tf
DVU0653
DVU2251
217 combiner
DVU1518
DVU2195
217 combiner
DVU1754 217 tf
DVU1754
DVU2097
217 combiner
DVU2567 217 tf
DVU2567
DVU3334
217 combiner
DVU3334
DVU0230
217 combiner
DVUA0024 217 tf
DVU0525 265 tf
DVU0653
DVU2251
265 combiner
DVU1754 265 tf
DVU1754
DVU2097
265 combiner
DVU2114 265 tf
DVU2686 265 tf
DVU2832 265 tf
DVU3229
DVU2832
265 combiner

Warning: DVU2070 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
413 1.80e+01 aAGCaCAaAA
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RegPredict
414 5.30e+03 TAtaattcaa.aTTGGcA.gTT
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RegPredict
505 1.30e+02 cGgctgCggCA..a
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RegPredict
506 4.00e+04 AAGAAAGA
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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 DVU2070

DVU2070 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Uncharacterized protein conserved in bacteria cog/ cog
binding go/ molecular_function
tol_pal_ybgF tigr/ tigrfam
Module neighborhood information for DVU2070

DVU2070 has total of 29 gene neighbors in modules 217, 265
Gene neighbors (29)
Gene Common Name Description Module membership
DVU0389 His/Glu/Gln/Arg/opine amino acid ABC transporter permease 217, 226
DVU0658 HSP20 family protein 124, 217
DVU0675 amino acid ABC transporter periplasmic amino acid-binding protein 102, 217
DVU0705 dctM TRAP transporter subunit DctM 92, 265
DVU1234 hypothetical protein DVU1234 102, 217
DVU1527 phage integrase family site specific recombinase 25, 265
DVU1697 hypothetical protein DVU1697 144, 265
DVU1726 hypothetical protein DVU1726 97, 265
DVU1727 hypothetical protein DVU1727 144, 265
DVU2057 hypothetical protein DVU2057 196, 217
DVU2064 2-nitropropane dioxygenase family oxidoreductase 208, 265
DVU2069 DNA processing protein DprA 208, 265
DVU2070 hypothetical protein 217, 265
DVU2071 hypothetical protein DVU2071 144, 265
DVU2084 oligopeptide-binding protein 102, 217
DVU2094 thiG thiazole synthase 102, 217
DVU2137 sucCD succinyl-CoA synthase, beta/subunit alphas 106, 265
DVU2153 tail fiber protein 217, 253
DVU2155 hypothetical protein DVU2155 165, 217
DVU2169 hypothetical protein DVU2169 1, 217
DVU2273 hypothetical protein DVU2273 144, 265
DVU2593 hypothetical protein DVU2593 134, 265
DVU2737 RNA methyltransferase 144, 265
DVU2875 DNA-binding protein 134, 265
DVU2877 hypothetical protein DVU2877 265, 316
DVU2878 adenine specific DNA methyltransferase 265, 340
DVU2907 umuD umuD protein 134, 265
DVU3354 None 19, 217
DVUA0127 None 167, 265
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 DVU2070
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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