Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2667

phosphate ABC transporter periplasmic phosphate-binding protein

CircVis
Functional Annotations (5)
Function System
ABC-type phosphate transport system, periplasmic component cog/ cog
transport go/ biological_process
ABC transporters kegg/ kegg pathway
Two-component system kegg/ kegg pathway
ptsS_2 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2667
(Mouseover regulator name to see its description)

DVU2667 is regulated by 16 influences and regulates 0 modules.
Regulators for DVU2667 (16)
Regulator Module Operator
DVU0309
DVU0539
137 combiner
DVU0309
DVU3334
137 combiner
DVU1754
DVU2802
137 combiner
DVU2114
DVU1760
137 combiner
DVU2799 137 tf
DVU2802
DVU0539
137 combiner
DVU2960
DVU0916
137 combiner
DVUA0151
DVU3066
137 combiner
DVU0813
DVU0230
119 combiner
DVU0813
DVU1517
119 combiner
DVU1572
DVU0269
119 combiner
DVU1572
DVU3255
119 combiner
DVU1788 119 tf
DVU2675
DVU3186
119 combiner
DVU2909
DVU1788
119 combiner
DVU3255
DVU1584
119 combiner

Warning: DVU2667 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
229 1.60e+03 CTgCTTGcaCggcA.gGctCGC
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RegPredict
230 1.30e+04 ATCATACATAcAA
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RegPredict
265 4.60e+03 CCccC.cgct.T.ccaCaTtCCgc
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RegPredict
266 1.70e+03 TTTcCGaaGTcGa
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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 DVU2667

DVU2667 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type phosphate transport system, periplasmic component cog/ cog
transport go/ biological_process
ABC transporters kegg/ kegg pathway
Two-component system kegg/ kegg pathway
ptsS_2 tigr/ tigrfam
Module neighborhood information for DVU2667

DVU2667 has total of 48 gene neighbors in modules 119, 137
Gene neighbors (48)
Gene Common Name Description Module membership
DVU0090 wcaG GDP-fucose synthetase 137, 236
DVU0093 glycosyl transferase domain-containing protein 119, 289
DVU0108 hypothetical protein DVU0108 137, 311
DVU0143 hypothetical protein DVU0143 95, 137
DVU0146 hypothetical protein DVU0146 53, 119
DVU0159 thioesterase family protein 57, 119
DVU0160 carbohydrate isomerase KpsF/GutQ family protein 57, 119
DVU0243 lipoprotein 57, 119
DVU0319 NAD-dependent epimerase/dehydratase 62, 119
DVU0333 hypothetical protein DVU0333 65, 137
DVU0359 HesB-like domain-containing protein 119, 226
DVU0376 hypothetical protein DVU0376 137, 305
DVU0378 thioredoxin 137, 236
DVU0380 sulfatase 119, 305
DVU0417 speA arginine decarboxylase 57, 119
DVU0418 lys1 saccharopine dehydrogenase 119, 236
DVU0831 PTS system transporter subunit IID 64, 119
DVU0842 hypothetical protein DVU0842 52, 137
DVU0843 hypothetical protein DVU0843 23, 137
DVU1096 argF ornithine carbamoyltransferase 137, 208
DVU1192 acylphosphatase 66, 119
DVU1455 hypothetical protein DVU1455 137, 188
DVU1467 hslU ATP-dependent protease ATP-binding subunit HslU 119, 227
DVU1722 hypothetical protein DVU1722 119, 167
DVU1728 hypothetical protein DVU1728 137, 315
DVU1770 hydB periplasmic 137, 294
DVU1956 heptosyltransferase family protein 137, 261
DVU2063 hypothetical protein DVU2063 137, 208
DVU2258 ruvC Holliday junction resolvase 65, 119
DVU2331 Smr family protein 137, 291
DVU2370 outer membrane protein OmpH 81, 137
DVU2420 hypothetical protein DVU2420 119, 236
DVU2476 gltA oxidoreductase 137, 326
DVU2486 acetyltransferase 119, 167
DVU2554 hypothetical protein DVU2554 119, 227
DVU2555 MATE efflux family protein 119, 120
DVU2641 lipoprotein 119, 254
DVU2658 hypothetical protein DVU2658 119, 215
DVU2659 exsB protein 119, 215
DVU2667 phosphate ABC transporter periplasmic phosphate-binding protein 119, 137
DVU2694 hypothetical protein DVU2694 137, 289
DVU2752 rhodanese-like domain-containing protein 97, 119
DVU2764 nitroreductase family protein 27, 137
DVU2876 terminase large subunit 7, 119
DVU2946 hypothetical protein DVU2946 137, 230
DVU3035 methyl-accepting chemotaxis protein 137, 229
DVU3159 gpsA NAD(P)H-dependent glycerol-3-phosphate dehydrogenase 137, 258
DVU3162 ABC transporter periplasmic substrate-binding protein 137, 193
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 DVU2667
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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