Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2298

glycine/betaine/L-proline ABC transporter permease

CircVis
Functional Annotations (6)
Function System
ABC-type proline/glycine betaine transport system, permease component cog/ cog
transport go/ biological_process
quaternary-ammonium-compound-transporting ATPase activity go/ molecular_function
glycine betaine/proline porter activity go/ molecular_function
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2298
(Mouseover regulator name to see its description)

DVU2298 is regulated by 26 influences and regulates 0 modules.
Regulators for DVU2298 (26)
Regulator Module Operator
DVU0063 235 tf
DVU0063
DVU1949
235 combiner
DVU0118 235 tf
DVU0118
DVU2690
235 combiner
DVU0682 235 tf
DVU0682
DVU1584
235 combiner
DVU1419 235 tf
DVU1572 235 tf
DVU1572
DVU2111
235 combiner
DVU2394 235 tf
DVU2547 235 tf
DVU0118 94 tf
DVU1572
DVU1730
94 combiner
DVU1572
DVU2319
94 combiner
DVU1572
DVU2423
94 combiner
DVU1572
DVU2956
94 combiner
DVU1572
DVU3313
94 combiner
DVU1745 94 tf
DVU1759 94 tf
DVU1759
DVU2275
94 combiner
DVU2111
DVU3186
94 combiner
DVU2275 94 tf
DVU2989 94 tf
DVU3167 94 tf
DVU3305 94 tf
DVU3313 94 tf

Warning: DVU2298 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
181 2.20e-02 ATCGCTtgTatGcaaGTtaaT
Loader icon
RegPredict
182 1.70e+02 CaTcaACCgga.a.aaggAAca.c
Loader icon
RegPredict
449 4.00e+02 ctcTTcCc.t
Loader icon
RegPredict
450 1.40e+04 AAAAAG
Loader icon
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 DVU2298

DVU2298 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
ABC-type proline/glycine betaine transport system, permease component cog/ cog
transport go/ biological_process
quaternary-ammonium-compound-transporting ATPase activity go/ molecular_function
glycine betaine/proline porter activity go/ molecular_function
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
Module neighborhood information for DVU2298

DVU2298 has total of 48 gene neighbors in modules 94, 235
Gene neighbors (48)
Gene Common Name Description Module membership
DVU0060 RND family efflux transporter MFP subunit 5, 94
DVU0061 multidrug resistance protein 5, 94
DVU0062 RND efflux system outer membrane lipoprotein 5, 94
DVU0063 MarR family transcriptional regulator 5, 94
DVU0224 hypothetical protein DVU0224 94, 156
DVU0399 hypothetical protein DVU0399 10, 235
DVU0503 pnp polynucleotide phosphorylase/polyadenylase 10, 235
DVU0507 hypothetical protein DVU0507 10, 235
DVU0508 infB translation initiation factor IF-2 10, 235
DVU0510 nusA transcription elongation factor NusA 10, 235
DVU0603 hypothetical protein DVU0603 5, 94
DVU0753 amino acid ABC transporter ATP-binding protein 235, 292
DVU0809 gatC glutamyl-tRNA(Gln) amidotransferase subunit C 29, 235
DVU0810 hypothetical protein DVU0810 29, 235
DVU1201 ribD riboflavin biosynthesis protein RibD 94, 169
DVU1247 hypothetical protein DVU1247 28, 235
DVU1248 argS arginyl-tRNA synthetase 29, 235
DVU1298 rpsL 30S ribosomal protein S12 10, 235
DVU1299 rpsG 30S ribosomal protein S7 10, 235
DVU1300 fusA-1 elongation factor G 10, 235
DVU1332 selD selenide, water dikinase, selenocysteine-containing 30, 94
DVU1571 rho transcription termination factor Rho 5, 235
DVU1622 purQ phosphoribosylformylglycinamidine synthase I 10, 235
DVU1775 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase 12, 94
DVU1791 GatB/Yqey family protein 28, 94
DVU1862 GGDEF domain-containing protein 94, 229
DVU1892 glycosyl transferase group 2 family protein 94, 277
DVU2130 hypothetical protein DVU2130 5, 94
DVU2216 infA translation initiation factor IF-1 235, 308
DVU2256 ruvA Holliday junction DNA helicase RuvA 94, 275
DVU2279 hypothetical protein DVU2279 94, 334
DVU2280 amino acid permease family protein 94, 334
DVU2298 glycine/betaine/L-proline ABC transporter permease 94, 235
DVU2299 glycine/betaine/L-proline ABC transporter ATP binding protein 5, 235
DVU2738 methyl-accepting chemotaxis protein 94, 179
DVU2771 hypothetical protein DVU2771 27, 94
DVU2913 lipoprotein 10, 235
DVU2914 prfA peptide chain release factor 1 10, 235
DVU3116 prfC peptide chain release factor 3 235, 278
DVU3151 tRNA modifying protein 5, 94
DVU3194 engA GTP-binding protein EngA 5, 94
DVU3204 purA adenylosuccinate synthetase 5, 94
DVU3205 transglycosylase 5, 94
DVU3206 phosphoribosylaminoimidazolecarboxamide formyltransferase 5, 235
DVU3307 ubiX 3-octaprenyl-4-hydroxybenzoate carboxy-lyase 29, 235
DVU3308 metallo-beta-lactamase family protein 10, 235
DVU3310 DEAD-box ATP dependent DNA helicase 10, 235
DVU3327 SMR family multidrug efflux pump 94, 279
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 DVU2298
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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