Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1068

branched-chain amino acid ABC transporter permease

CircVis
Functional Annotations (4)
Function System
ABC-type uncharacterized transport system, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1068
(Mouseover regulator name to see its description)

DVU1068 is regulated by 21 influences and regulates 0 modules.
Regulators for DVU1068 (21)
Regulator Module Operator
DVU0230
DVU1083
345 combiner
DVU0525 345 tf
DVU0539 345 tf
DVU0653
DVU2633
345 combiner
DVU0946 345 tf
DVU1754
DVU1561
345 combiner
DVU2036
DVU2633
345 combiner
DVU2114
DVU0110
345 combiner
DVU3142 345 tf
DVU3186
DVU0653
345 combiner
DVUA0151 345 tf
DVU0230 130 tf
DVU0525 130 tf
DVU0525
DVU1745
130 combiner
DVU0653
DVU2633
130 combiner
DVU1517 130 tf
DVU1754 130 tf
DVU2567 130 tf
DVU2690 130 tf
DVU3142 130 tf
DVU3186
DVU0653
130 combiner

Warning: DVU1068 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
251 1.90e+03 GatGtCAccGAGGa
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RegPredict
252 2.50e+03 CAcGtAtCAtc
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RegPredict
655 2.40e+03 CCgtTTC
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RegPredict
656 5.70e+03 tGttgc.ggcATGa.cg.cgaTGc
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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 DVU1068

DVU1068 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type uncharacterized transport system, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
Module neighborhood information for DVU1068

DVU1068 has total of 21 gene neighbors in modules 130, 345
Gene neighbors (21)
Gene Common Name Description Module membership
DVU0365 hypothetical protein DVU0365 130, 210
DVU0375 Glu/Leu/Phe/Val dehydrogenase family protein 72, 130
DVU0479 serine/threonine protein kinase 160, 345
DVU0497 hypothetical protein DVU0497 85, 130
DVU0538 AP endonuclease 295, 345
DVU0887 transglycosylase 21, 130
DVU1068 branched-chain amino acid ABC transporter permease 130, 345
DVU1080 iron-sulfur cluster-binding protein 85, 345
DVU1156 sigma-54 dependent transcriptional regulator /response regulator 97, 345
DVU1490 tail tape measure protein 21, 130
DVU1829 hypothetical protein DVU1829 130, 210
DVU2095 thiS thiamine biosynthesis protein ThiS 99, 345
DVU2159 hypothetical protein DVU2159 130, 253
DVU2161 hypothetical protein DVU2161 130, 210
DVU2266 hypothetical protein DVU2266 130, 210
DVU2424 hypothetical protein DVU2424 203, 345
DVU2758 hypothetical protein DVU2758 124, 345
DVU2786 hypothetical protein DVU2786 210, 345
DVU3129 hypothetical protein DVU3129 70, 130
DVUA0009 nitrogenase molybdenum-cofactor biosynthesis protein NifE 130, 276
DVUA0129 cas3 CRISPR-associated helicase Cas3 domain-containing protein 202, 345
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 DVU1068
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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