Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2567

hypothetical protein DVU2567

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2567
(Mouseover regulator name to see its description)

DVU2567 is regulated by 21 influences and regulates 46 modules.
Regulators for DVU2567 (21)
Regulator Module Operator
DVU0529
DVU0525
3 combiner
DVU0653 3 tf
DVU1517 3 tf
DVU1561
DVU0525
3 combiner
DVU1561
DVUA0024
3 combiner
DVU1754 3 tf
DVU2086
DVU1517
3 combiner
DVU2195 3 tf
DVU2532
DVU0110
3 combiner
DVU2532
DVU0653
3 combiner
DVU2832 3 tf
DVU3142 3 tf
DVU3167 3 tf
DVU1063 270 tf
DVU1754
DVU1561
270 combiner
DVU1788
DVU0804
270 combiner
DVU1949 270 tf
DVU2788
DVU0916
270 combiner
DVU2799 270 tf
DVU2832
DVU1745
270 combiner
DVU2909
DVU1517
270 combiner

Warning: DVU2567 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
5 4.80e+02 aat.gaTcaC.gAAAGaAAga
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RegPredict
6 2.30e+03 tCgaGcgtgaaCcC.ACgCC
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RegPredict
515 4.00e+03 gCAAcGcaACC
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RegPredict
516 2.10e+01 AttCgtTgaC.aaaTtCTG.AAG
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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 DVU2567

DVU2567 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
Module neighborhood information for DVU2567

DVU2567 has total of 42 gene neighbors in modules 3, 270
Gene neighbors (42)
Gene Common Name Description Module membership
DVU0230 transcriptional regulator cII 3, 156
DVU0422 sensory box protein 208, 270
DVU0426 chromate transport family protein 3, 32
DVU0527 maF Maf-like protein 13, 270
DVU0668 methyl-accepting chemotaxis protein 193, 270
DVU0786 penicillin-binding protein 28, 270
DVU1044 guaB inosine-5`-monophosphate dehydrogenase 28, 270
DVU1240 hypothetical protein DVU1240 28, 270
DVU1251 hypothetical protein DVU1251 65, 270
DVU1258 glnN glutamine synthetase, type III 254, 270
DVU1273 type II/III secretion system protein 65, 270
DVU1429 ychF GTP-dependent nucleic acid-binding protein EngD 254, 270
DVU1482 hypothetical protein DVU1482 3, 100
DVU1694 C4-type zinc finger DksA/TraR family protein 84, 270
DVU1699 hypothetical protein DVU1699 3, 256
DVU1703 type I restriction-modification enzyme, R subunit 118, 270
DVU1878 ltaE threonine aldolase 65, 270
DVU1879 glycosyl transferase group 1 family protein 65, 270
DVU1890 hemC porphobilinogen deaminase 28, 270
DVU1897 glyS glycyl-tRNA synthetase subunit beta 28, 270
DVU1898 glyQ glycyl-tRNA synthetase subunit alpha 28, 270
DVU1949 nifA-1 nif-specific regulatory protein 28, 270
DVU1951 indolepyruvate ferredoxin oxidoreductase subunit alpha 28, 270
DVU1957 hypothetical protein DVU1957 3, 193
DVU2043 hypothetical protein DVU2043 270, 273
DVU2158 hypothetical protein DVU2158 3, 72
DVU2249 hypothetical protein DVU2249 3, 244
DVU2296 mtgA monofunctional biosynthetic peptidoglycan transglycosylase 3, 244
DVU2317 methyl-accepting chemotaxis protein 270, 311
DVU2343 amino acid ABC transporter ATP-binding protein 3, 28
DVU2432 sensory box protein 3, 295
DVU2567 hypothetical protein DVU2567 3, 270
DVU2579 hypothetical protein 208, 270
DVU2678 RNA pseudouridine synthase family protein 84, 270
DVU3052 ABC transporter ATP-binding protein 221, 270
DVU3066 DNA-binding protein 65, 270
DVU3078 hypothetical protein DVU3078 3, 85
DVU3249 lipoprotein 3, 295
DVU3251 HPP family membrane protein 3, 264
DVU3258 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase 82, 270
DVU3279 cobT nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase 254, 270
DVUA0046 glycosyl transferase, group 2 family protein 3, 61
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 DVU2567
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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