Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1026 uraA

uracil permease

CircVis
Functional Annotations (6)
Function System
Xanthine/uracil permeases cog/ cog
uracil phosphoribosyltransferase activity go/ molecular_function
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ncs2 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1026
(Mouseover regulator name to see its description)

DVU1026 is regulated by 29 influences and regulates 0 modules.
Regulators for DVU1026 uraA (29)
Regulator Module Operator
DVU0936 344 tf
DVU1547
DVUA0024
344 combiner
DVU2036 344 tf
DVU2036
DVU2275
344 combiner
DVU2036
DVU2582
344 combiner
DVU2086 344 tf
DVU2275 344 tf
DVU2423
DVU3381
344 combiner
DVU2547
DVU2588
344 combiner
DVU2588
DVU1547
344 combiner
DVU2836 344 tf
DVU3142
DVU0813
344 combiner
DVU3381 344 tf
DVUA0151 344 tf
DVU0653 75 tf
DVU1063 75 tf
DVU1419 75 tf
DVU1584
DVU0653
75 combiner
DVU2036 75 tf
DVU2036
DVU1584
75 combiner
DVU2036
DVU2097
75 combiner
DVU2036
DVU2275
75 combiner
DVU2195 75 tf
DVU2423
DVU2588
75 combiner
DVU2423
DVU3142
75 combiner
DVU2547
DVU2588
75 combiner
DVU2588
DVU1142
75 combiner
DVU3381 75 tf
DVUA0151
DVU1547
75 combiner

Warning: DVU1026 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
147 5.50e+00 cTgTtgCATC.gacGccCc.tGgc
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RegPredict
148 4.40e+01 tTtTtctaga.Gtc
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RegPredict
653 9.80e+00 TacaAcct.tgggAaAaggag
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RegPredict
654 1.10e+03 TtttAAaaAAA
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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 DVU1026

DVU1026 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Xanthine/uracil permeases cog/ cog
uracil phosphoribosyltransferase activity go/ molecular_function
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ncs2 tigr/ tigrfam
Module neighborhood information for DVU1026

DVU1026 has total of 43 gene neighbors in modules 75, 344
Gene neighbors (43)
Gene Common Name Description Module membership
DVU0014 infA translation initiation factor IF-1 78, 344
DVU0450 ribF riboflavin biosynthesis protein RibF 75, 278
DVU0451 chloride channel family protein 75, 327
DVU0746 ABC transporter permease 75, 126
DVU0764 hup-2 DNA-binding protein HU 166, 344
DVU0784 hypothetical protein DVU0784 75, 344
DVU0785 rodA rod shape-determining protein RodA 75, 294
DVU0787 hypothetical protein DVU0787 75, 336
DVU0841 aspartate aminotransferase 146, 344
DVU0895 RecD/TraA family helicase 75, 78
DVU0968 amino acid ABC transporter ATP-binding protein 336, 344
DVU1008 hypothetical protein DVU1008 78, 344
DVU1025 upp uracil phosphoribosyltransferase 323, 344
DVU1026 uraA uracil permease 75, 344
DVU1092 sodium-dependent symporter family protein 75, 344
DVU1260 outer membrane protein P1 288, 344
DVU1290 nitrate reductase subunit gamma 255, 344
DVU1323 secY preprotein translocase subunit SecY 221, 344
DVU1346 xseA exodeoxyribonuclease VII large subunit 75, 195
DVU1349 geranylgeranyl diphosphate synthase 75, 195
DVU1355 hypothetical protein DVU1355 75, 128
DVU1357 hypothetical protein DVU1357 75, 87
DVU1797 ksgA dimethyladenosine transferase 75, 150
DVU1798 hypothetical protein DVU1798 75, 98
DVU1806 mgtE magnesium transporter 44, 75
DVU1808 nadA quinolinate synthetase 75, 258
DVU1809 nadB L-aspartate oxidase 75, 98
DVU1928 lspA lipoprotein signal peptidase 52, 75
DVU1935 phosphonate ABC transporter permease 75, 336
DVU1936 phosphonate ABC transporter ATP-binding protein 75, 306
DVU2032 ERF family protein 196, 344
DVU2033 hypothetical protein DVU2033 266, 344
DVU2035 plasmid stabilization system family protein 273, 344
DVU2254 thyX FAD-dependent thymidylate synthase 75, 228
DVU2255 ruvB Holliday junction DNA helicase RuvB 75, 228
DVU2339 ribosomal protein L11 methyltransferase 29, 75
DVU2682 DedA family protein 121, 344
DVU2696 hypothetical protein DVU2696 266, 344
DVU2697 hypothetical protein DVU2697 266, 344
DVU2901 pyrB aspartate carbamoyltransferase catalytic subunit 141, 344
DVU2931 sensory box histidine kinase 75, 262
DVU3165 hypothetical protein DVU3165 75, 336
DVU3210 thrC threonine synthase 52, 344
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 DVU1026
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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