Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3164

ABC transporter permease

CircVis
Functional Annotations (5)
Function System
ABC-type sugar transport system, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3164
(Mouseover regulator name to see its description)

DVU3164 is regulated by 28 influences and regulates 0 modules.
Regulators for DVU3164 (28)
Regulator Module Operator
DVU0030
DVUA0057
174 combiner
DVU0057
DVU0230
174 combiner
DVU0594
DVU0653
174 combiner
DVU0606
DVU0653
174 combiner
DVU0653
DVU0679
174 combiner
DVU0653
DVU2251
174 combiner
DVU0813
DVU0230
174 combiner
DVU2423
DVU2832
174 combiner
DVU2588
DVU0813
174 combiner
DVU2588
DVU1964
174 combiner
DVU3167 174 tf
DVU3313
DVU2588
174 combiner
DVUA0024 174 tf
DVUA0057 174 tf
DVU0606
DVU3255
336 combiner
DVU0682
DVU3255
336 combiner
DVU1584
DVU3023
336 combiner
DVU1754 336 tf
DVU2086 336 tf
DVU2423
DVU2588
336 combiner
DVU2588
DVU3381
336 combiner
DVU2836 336 tf
DVU3023 336 tf
DVU3142
DVU0813
336 combiner
DVU3142
DVU1419
336 combiner
DVU3255
DVU0594
336 combiner
DVU3255
DVU1744
336 combiner
DVUA0151 336 tf

Warning: DVU3164 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
333 7.60e+03 GAagAaCt.gcCcaT
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RegPredict
334 9.10e+03 AcGaTACGGtaa.Gc.cgTC
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RegPredict
637 9.50e+02 AtcGtGctTTc
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RegPredict
638 6.60e+02 tTcTaTgttTtcaatttAT
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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 DVU3164

DVU3164 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type sugar transport system, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
Module neighborhood information for DVU3164

DVU3164 has total of 41 gene neighbors in modules 174, 336
Gene neighbors (41)
Gene Common Name Description Module membership
DVU0169 oligopeptide/dipeptide ABC transporter periplasmic oligopeptide/dipeptide-binding protein 174, 250
DVU0362 hypothetical protein DVU0362 174, 334
DVU0480 hypothetical protein DVU0480 174, 206
DVU0506 DHH family protein 163, 336
DVU0569 sigma-54 dependent transcriptional regulator 162, 174
DVU0654 U32 family peptidase 172, 174
DVU0787 hypothetical protein DVU0787 75, 336
DVU0788 mreC rod shape-determining protein MreC 300, 336
DVU0911 truA tRNA pseudouridine synthase A 30, 174
DVU0967 His/Glu/Gln/Arg/opine ABC transporter permease 154, 336
DVU0968 amino acid ABC transporter ATP-binding protein 336, 344
DVU1172 hypothetical protein DVU1172 33, 174
DVU1271 general secretion pathway protein F 174, 221
DVU1532 coaD phosphopantetheine adenylyltransferase 135, 336
DVU1635 hypothetical protein DVU1635 174, 188
DVU1671 ABC transporter ATP-binding protein/permease 154, 336
DVU1673 acyltransferase 282, 336
DVU1776 hypothetical protein DVU1776 126, 336
DVU1935 phosphonate ABC transporter permease 75, 336
DVU1961 cheW-3 chemotaxis protein CheW 174, 286
DVU2036 CopG family transcriptinal regulator 291, 336
DVU2144 gap-2 glyceraldehyde 3-phosphate dehydrogenase 54, 174
DVU2322 UTP--glucose-1-phosphate uridylyltransferase 23, 174
DVU2368 fabZ (3R)-hydroxymyristoyl-ACP dehydratase 52, 174
DVU2369 lpxD UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase 174, 251
DVU2374 lolD lipoprotein releasing system, ATP-binding protein 237, 336
DVU2375 lipoprotein releasing system, permease 300, 336
DVU2576 oligopeptide ABC transporter ATP-binding protein 174, 318
DVU2693 hypothetical protein DVU2693 174, 330
DVU2905 iron-containing alcohol dehydrogenase 83, 174
DVU3013 glycosyl transferase group 2 family protein 162, 174
DVU3022 sensory box histidine kinase/response regulator 162, 174
DVU3046 glycosyl transferase group 1 family protein 174, 206
DVU3050 hypothetical protein DVU3050 174, 278
DVU3069 hypothetical protein DVU3069 237, 336
DVU3109 iron-sulfur cluster-binding protein 174, 278
DVU3163 ABC transporter permease 174, 251
DVU3164 ABC transporter permease 174, 336
DVU3165 hypothetical protein DVU3165 75, 336
DVU3179 ispB octaprenyl-diphosphate synthase 172, 174
DVU3181 purL phosphoribosylformylglycinamidine synthase II 81, 174
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 DVU3164
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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