Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2461

oligopeptide ABC transporter permease

CircVis
Functional Annotations (6)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
alkaline phosphatase activity go/ molecular_function
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 DVU2461
(Mouseover regulator name to see its description)

DVU2461 is regulated by 17 influences and regulates 0 modules.
Regulators for DVU2461 (17)
Regulator Module Operator
DVU0653 9 tf
DVU1561 9 tf
DVU1561
DVU0230
9 combiner
DVU2275 9 tf
DVU3023 9 tf
DVU3167
DVU0569
9 combiner
DVU3167
DVU1730
9 combiner
DVUA0024 9 tf
DVU1063 69 tf
DVU1063
DVU2934
69 combiner
DVU1744 69 tf
DVU2633
DVU1730
69 combiner
DVU2788
DVU1744
69 combiner
DVU3066
DVU2690
69 combiner
DVU3111
DVU1402
69 combiner
DVU3142
DVU0529
69 combiner
DVUA0100
DVU1063
69 combiner

Warning: DVU2461 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
17 1.20e+04 agcgGgCaTgG
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RegPredict
18 1.30e+04 TcCTGaaAacC
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RegPredict
135 1.60e+02 ttCattcTcttttccgGtcgCgca
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RegPredict
136 4.40e+03 ATGACa
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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 DVU2461

DVU2461 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components cog/ cog
alkaline phosphatase activity go/ molecular_function
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
Module neighborhood information for DVU2461

DVU2461 has total of 62 gene neighbors in modules 9, 69
Gene neighbors (62)
Gene Common Name Description Module membership
DVU0038 acyltransferase domain-containing protein 69, 161
DVU0084 aIF-2BI family translation initiation factor 9, 23
DVU0087 hypothetical protein DVU0087 9, 44
DVU0088 panF sodium/panthothenate symporter 9, 69
DVU0091 hypothetical protein DVU0091 9, 327
DVU0101 UbiE/COQ5 family methlytransferase 69, 247
DVU0104 cation ABC transporter permease 69, 162
DVU0141 M50 family peptidase 9, 223
DVU0142 trpS tryptophanyl-tRNA synthetase 9, 180
DVU0236 phage integrase family site specific recombinase 54, 69
DVU0249 hypothetical protein DVU0249 69, 181
DVU0257 acetyltransferase 37, 69
DVU0323 folD bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 9, 223
DVU0324 hypothetical protein DVU0324 9, 181
DVU0345 hypothetical protein DVU0345 46, 69
DVU0651 hypothetical protein DVU0651 9, 334
DVU0794 fabI enoyl-ACP reductase 9, 113
DVU0859 hypothetical protein DVU0859 69, 162
DVU1029 hisC histidinol-phosphate aminotransferase 9, 223
DVU1036 hypothetical protein DVU1036 69, 334
DVU1113 hypothetical protein DVU1113 69, 185
DVU1165 pyridine nucleotide-disulfide oxidoreductase 69, 330
DVU1185 colicin V production family protein 9, 180
DVU1189 hypothetical protein DVU1189 9, 277
DVU1213 rhomboid family protein 69, 120
DVU1269 hypothetical protein DVU1269 69, 172
DVU1369 hypothetical protein DVU1369 9, 126
DVU1370 hypothetical protein DVU1370 9, 141
DVU1389 hypothetical protein DVU1389 69, 162
DVU1391 hypothetical protein DVU1391 69, 87
DVU1435 hypothetical protein DVU1435 69, 87
DVU1459 hypothetical protein DVU1459 9, 334
DVU1540 purU formyltetrahydrofolate deformylase 9, 223
DVU1860 lnt apolipoprotein N-acyltransferase 9, 214
DVU1863 flagellar synthesis regulator FleN 9, 113
DVU1958 sensory box histidine kinase 69, 192
DVU2234 hypothetical protein DVU2234 69, 185
DVU2257 hypothetical protein DVU2257 9, 214
DVU2276 hypothetical protein DVU2276 69, 334
DVU2320 3-octaprenyl-4-hydroxybenzoate carboxy-lyase 9, 316
DVU2366 hypothetical protein DVU2366 69, 155
DVU2408 hypothetical protein DVU2408 69, 269
DVU2461 oligopeptide ABC transporter permease 9, 69
DVU2465 hypothetical protein DVU2465 69, 245
DVU2520 hypothetical protein DVU2520 69, 185
DVU2558 bioB biotin synthase 9, 327
DVU2570 GGDEF domain/HAMP domain-containing protein 69, 247
DVU2594 hypothetical protein DVU2594 69, 275
DVU2634 hypothetical protein DVU2634 5, 9
DVU2660 hypothetical protein DVU2660 69, 275
DVU2700 hypothetical protein DVU2700 33, 69
DVU2780 hypothetical protein DVU2780 69, 141
DVU2823 TRAP transporter subunit DctMQ 69, 181
DVU2908 hypothetical protein DVU2908 69, 334
DVU2910 hypothetical protein DVU2910 69, 113
DVU2953 GntR family transcriptional regulator 35, 69
DVU2954 GGDEF domain-containing protein 69, 334
DVU2955 hypothetical protein DVU2955 69, 334
DVU3017 hypothetical protein DVU3017 69, 87
DVU3040 hypothetical protein DVU3040 69, 181
DVU3297 tryptophan-specific transport protein 9, 334
DVU3386 permease 69, 222
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 DVU2461
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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