Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3139

solute-binding family 1 protein

CircVis
Functional Annotations (4)
Function System
ABC-type amino acid transport/signal transduction systems, periplasmic component/domain cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3139
(Mouseover regulator name to see its description)

DVU3139 is regulated by 19 influences and regulates 0 modules.
Regulators for DVU3139 (19)
Regulator Module Operator
DVU0230 80 tf
DVU0230
DVU1083
80 combiner
DVU0525 80 tf
DVU1517 80 tf
DVU1754 80 tf
DVU2690 80 tf
DVU2832 80 tf
DVU2836
DVU0653
80 combiner
DVUA0024
DVU0529
80 combiner
DVU0230
DVU1083
41 combiner
DVU0525 41 tf
DVU0539 41 tf
DVU1754 41 tf
DVU2036
DVU2633
41 combiner
DVU2588 41 tf
DVU3142 41 tf
DVU3186
DVU0569
41 combiner
DVUA0143 41 tf
DVUA0151 41 tf

Warning: DVU3139 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
81 1.70e+03 tGaCAAaA
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RegPredict
82 1.10e+04 TATAAA
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RegPredict
157 1.00e+03 aCaag.acgAcaCc.CggacgaaA
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RegPredict
158 9.50e+03 aaatcaaGtAAgcCgGacTt
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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 DVU3139

DVU3139 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type amino acid transport/signal transduction systems, periplasmic component/domain cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
outer membrane-bounded periplasmic space go/ cellular_component
Module neighborhood information for DVU3139

DVU3139 has total of 23 gene neighbors in modules 41, 80
Gene neighbors (23)
Gene Common Name Description Module membership
DVU0081 sensory box histidine kinase/response regulator 36, 41
DVU0115 aroE shikimate 5-dehydrogenase 41, 295
DVU0366 5-formyltetrahydrofolate cyclo-ligase family protein 41, 210
DVU1053 hypothetical protein DVU1053 80, 338
DVU1107 tail tape measure protein 80, 259
DVU1162 hypothetical protein DVU1162 80, 242
DVU1417 hypothetical protein DVU1417 79, 80
DVU1504 terminase small subunit 80, 152
DVU1513 hypothetical protein DVU1513 80, 129
DVU1515 type II DNA modification methyltransferase 80, 129
DVU1516 hypothetical protein DVU1516 80, 129
DVU1735 hypothetical protein DVU1735 41, 102
DVU1969 hypothetical protein DVU1969 80, 299
DVU2578 response regulator 41, 210
DVU2604 hypothetical protein DVU2604 80, 213
DVU2614 hypothetical protein DVU2614 41, 90
DVU2645 Na+/H+ antiporter family protein 80, 244
DVU2647 L-PSP family endoribonuclease 20, 80
DVU2701 hypothetical protein DVU2701 41, 168
DVU2720 hypothetical protein DVU2720 20, 80
DVU2860 hypothetical protein DVU2860 41, 58
DVU2865 lipoprotein 36, 41
DVU3139 solute-binding family 1 protein 41, 80
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 DVU3139
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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