Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2479

phosphate ABC transporter permease

CircVis
Functional Annotations (7)
Function System
ABC-type phosphate transport system, permease component cog/ cog
inorganic phosphate transmembrane transporter activity go/ molecular_function
phosphate ion transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
3a0107s02c tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2479
(Mouseover regulator name to see its description)

DVU2479 is regulated by 20 influences and regulates 0 modules.
Regulators for DVU2479 (20)
Regulator Module Operator
DVU0269
DVU2633
211 combiner
DVU0309
DVU0744
211 combiner
DVU0309
DVU3142
211 combiner
DVU1572
DVU0936
211 combiner
DVU1572
DVU2106
211 combiner
DVU2423
DVU0621
211 combiner
DVU2567
DVU0621
211 combiner
DVU2686
DVU3255
211 combiner
DVU2909
DVU0621
211 combiner
DVU3186
DVU2106
211 combiner
DVU1645
DVU3193
304 combiner
DVU1674
DVU3095
304 combiner
DVU1674
DVU3186
304 combiner
DVU2319 304 tf
DVU2547
DVU2934
304 combiner
DVU2644 304 tf
DVU2644
DVU2799
304 combiner
DVU2934
DVU0621
304 combiner
DVU3084 304 tf
DVU3193
DVU2114
304 combiner

Warning: DVU2479 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
403 1.30e+00 tGccgTG.CtGacg
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RegPredict
404 2.90e+04 agGgCAtCcgtCccG
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RegPredict
581 5.20e+04 TcCATGTCacA
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RegPredict
582 2.00e+04 CggaTGCCCTG
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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 DVU2479

DVU2479 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
ABC-type phosphate transport system, permease component cog/ cog
inorganic phosphate transmembrane transporter activity go/ molecular_function
phosphate ion transport go/ biological_process
Gram-negative-bacterium-type cell wall go/ cellular_component
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
3a0107s02c tigr/ tigrfam
Module neighborhood information for DVU2479

DVU2479 has total of 57 gene neighbors in modules 211, 304
Gene neighbors (57)
Gene Common Name Description Module membership
DVU0031 AzlC family protein 38, 211
DVU0032 hypothetical protein DVU0032 112, 211
DVU0055 ispH hydroxymethylbutenyl pyrophosphate reductase 185, 304
DVU0187 GGDEF domain-containing protein 258, 304
DVU0245 protein phosphatase 46, 304
DVU0393 ung uracil-DNA glycosylase 51, 211
DVU0412 potassium uptake protein TrkA 46, 304
DVU0584 transposase 105, 304
DVU0647 iron compound ABC transporter periplasmic iron compount-binding protein 23, 211
DVU0655 phosphotransferase domain-containing protein 201, 211
DVU0687 tungsten-containing aldehyde:ferredoxin oxidoreductase 82, 304
DVU0689 rnhA ribonuclease H 82, 304
DVU0749 DNA-binding response regulator 26, 304
DVU0757 hypothetical protein DVU0757 28, 211
DVU0814 bacterioferritin comigratory protein 112, 211
DVU0897 RNA modification protein 172, 304
DVU0898 hypothetical protein DVU0898 172, 304
DVU0900 gmk guanylate kinase 172, 304
DVU0901 pyrF orotidine 5`-phosphate decarboxylase 32, 304
DVU0922 cytochrome c family protein 304, 307
DVU0978 ABC transporter periplasmic substrate-binding protein 76, 211
DVU0982 hypothetical protein DVU0982 57, 211
DVU0996 hypothetical protein DVU0996 304, 307
DVU1188 hypothetical protein DVU1188 211, 304
DVU1401 hypothetical protein DVU1401 57, 211
DVU1437 hypothetical protein DVU1437 201, 211
DVU1445 flagellar hook-length control domain-containing protein 211, 311
DVU1536 Slt family transglycosylase 12, 304
DVU1938 hypothetical protein DVU1938 208, 211
DVU2092 thiamine biosynthesis protein ThiF 161, 304
DVU2365 hypothetical protein DVU2365 304, 315
DVU2419 hypothetical protein DVU2419 211, 260
DVU2477 pstS phosphate ABC transporter periplasmic phosphate-binding protein PstS 211, 304
DVU2479 phosphate ABC transporter permease 211, 304
DVU2543 hydroxylamine reductase 153, 304
DVU2739 pyruvate phosphate dikinase PEP/pyruvate binding subunit 112, 304
DVU2749 cobL precorrin-6Y C5,15-methyltransferase (decarboxylating) 166, 304
DVU2822 TRAP transporter solute receptor DctP 82, 211
DVU2824 formate acetyltransferase 82, 211
DVU2886 AraC family transcriptional regulator 251, 304
DVU2947 anaerobic ribonucleoside triphosphate reductase 81, 304
DVU2961 hypothetical protein DVU2961 285, 304
DVU3010 aminotransferase 112, 304
DVU3014 asparagine synthetase, glutamine-hydrolyzing 22, 211
DVU3073 hypothetical protein DVU3073 99, 211
DVU3209 hypothetical protein DVU3209 112, 211
DVU3219 hypothetical protein DVU3219 211, 254
DVU3223 aspB aspartate aminotransferase 211, 278
DVU3229 fliA RNA polymerase sigma factor for flagellar operon FliA 251, 304
DVU3284 L-lactate permease 211, 311
DVU3360 ParB family protein 76, 211
DVU3361 ADP-heptose synthase 211, 278
DVUA0072 glycosyl transferase, group 1 family protein 255, 304
DVUA0086 response regulator 131, 211
DVUA0097 radical SAM domain-containing protein 201, 211
DVUA0114 hypothetical protein DVUA0114 136, 211
DVUA0117 escJ type III secretion lipoprotein 136, 211
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 DVU2479
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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