Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0009

TRAP transporter subunit DctM

CircVis
Functional Annotations (3)
Function System
TRAP-type C4-dicarboxylate transport system, large permease component cog/ cog
integral to membrane go/ cellular_component
dctM tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0009
(Mouseover regulator name to see its description)

DVU0009 is regulated by 19 influences and regulates 0 modules.
Regulators for DVU0009 (19)
Regulator Module Operator
DVU0594 181 tf
DVU0594
DVU0749
181 combiner
DVU1518
DVU2527
181 combiner
DVU1754
DVU2527
181 combiner
DVU2527
DVU3066
181 combiner
DVU2644
DVU0539
181 combiner
DVU2644
DVU1561
181 combiner
DVU2953 181 tf
DVU0230 341 tf
DVU0594 341 tf
DVU1949
DVU2251
341 combiner
DVU2644
DVU0063
341 combiner
DVU2644
DVU0653
341 combiner
DVU2644
DVU2106
341 combiner
DVU2644
DVU2251
341 combiner
DVU2644
DVU2527
341 combiner
DVU2827 341 tf
DVU2836 341 tf
DVUA0151 341 tf

Warning: DVU0009 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
345 5.70e+02 atAAagTCaA.ctaaAAcAcA
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RegPredict
346 1.30e+01 GAcGGcAaggc
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RegPredict
647 1.10e+02 CcTtgCCtttGtCgt
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RegPredict
648 2.90e+04 cacacGcaacGcatGAcagtgCCC
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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 DVU0009

DVU0009 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
TRAP-type C4-dicarboxylate transport system, large permease component cog/ cog
integral to membrane go/ cellular_component
dctM tigr/ tigrfam
Module neighborhood information for DVU0009

DVU0009 has total of 50 gene neighbors in modules 181, 341
Gene neighbors (50)
Gene Common Name Description Module membership
DVU0009 TRAP transporter subunit DctM 181, 341
DVU0067 hypothetical protein DVU0067 181, 341
DVU0102 cation ABC transporter periplasmic binding protein 181, 341
DVU0126 ABC transporter ATP-binding protein 33, 181
DVU0249 hypothetical protein DVU0249 69, 181
DVU0308 hypothetical protein DVU0308 181, 280
DVU0324 hypothetical protein DVU0324 9, 181
DVU0346 hypothetical protein DVU0346 162, 181
DVU0351 cytidine 5'monophosphate N-acetylneuraminic acid synthetase /polysaccharide biosynthesis protein 234, 341
DVU0363 pabB para-aminobenzoate synthase, component I 181, 334
DVU0381 nhaC-1 Na+/H+ antiporter NhaC 37, 341
DVU0448 gmd GDP-mannose 4,6-dehydratase 308, 341
DVU0736 purN phosphoribosylglycinamide formyltransferase 55, 181
DVU1035 glucokinase 234, 341
DVU1037 mercuric reductase 181, 192
DVU1128 lysozyme 231, 341
DVU1129 hypothetical protein DVU1129 231, 341
DVU1173 mviN-1 integral membrane protein MviN 33, 181
DVU1239 hypothetical protein DVU1239 234, 341
DVU1446 heptosyltransferase family protein 318, 341
DVU1451 response regulator 318, 341
DVU1508 hypothetical protein DVU1508 234, 341
DVU1604 hypothetical protein DVU1604 37, 181
DVU1662 permease 154, 181
DVU1683 hypothetical protein DVU1683 181, 318
DVU1744 DNA-binding protein 33, 181
DVU1810 hypothetical protein DVU1810 245, 341
DVU1858 cold shock domain-containing protein 234, 341
DVU2277 hypothetical protein DVU2277 261, 341
DVU2283 hypothetical protein DVU2283 234, 341
DVU2336 carboxyl-terminal protease 234, 341
DVU2358 hypothetical protein DVU2358 181, 275
DVU2618 hypothetical protein DVU2618 35, 181
DVU2730 tail fiber protein 181, 247
DVU2743 livH high-affinity branched-chain amino acid ABC ransporter, permease 181, 275
DVU2761 hypothetical protein DVU2761 181, 214
DVU2787 hypothetical protein DVU2787 48, 181
DVU2823 TRAP transporter subunit DctMQ 69, 181
DVU2855 tail/DNA circulation protein 314, 341
DVU2871 minor capsid protein C 181, 341
DVU2874 hypothetical protein DVU2874 234, 341
DVU2992 glycosyl transferase group 2 family protein 222, 341
DVU3040 hypothetical protein DVU3040 69, 181
DVU3043 hypothetical protein DVU3043 181, 334
DVU3081 hypothetical protein DVU3081 181, 341
DVU3108 nhaC-2 Na+/H+ antiporter NhaC 181, 341
DVU3110 oxidoreductase 234, 341
DVU3267 hypothetical protein DVU3267 181, 341
DVU3325 hypothetical protein DVU3325 234, 341
DVUA0096 major facilitator superfamily protein 234, 341
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 DVU0009
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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