Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2695

hypothetical protein DVU2695

CircVis
Functional Annotations (1)
Function System
Mu-like prophage protein gp16 cog/ cog
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2695
(Mouseover regulator name to see its description)

DVU2695 is regulated by 18 influences and regulates 0 modules.
Regulators for DVU2695 (18)
Regulator Module Operator
DVU0525 40 tf
DVU0653
DVU2251		 40 combiner
DVU0653
DVU2633		 40 combiner
DVU1754 40 tf
DVU2588 40 tf
DVU2832 40 tf
DVU3334
DVU0230		 40 combiner
DVU0030
DVU2567		 72 combiner
DVU0230
DVU0621		 72 combiner
DVU0525 72 tf
DVU0653 72 tf
DVU0653
DVU2633		 72 combiner
DVU1517 72 tf
DVU1754 72 tf
DVU2114 72 tf
DVU2832 72 tf
DVU3186
DVU0653		 72 combiner
DVUA0057 72 tf

Warning: DVU2695 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
79 5.90e+01 atcctGacgAGcaGc.Gaa
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 RegPredict
80 1.70e+02 TGCGGGGcggtcGtCtggcggTG
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 RegPredict
141 5.50e+00 acGgagatGAc
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 RegPredict
142 2.70e+03 tT.ctTt.at.ttctGttt
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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 DVU2695

DVU2695 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Mu-like prophage protein gp16 cog/ cog
Module neighborhood information for DVU2695

DVU2695 has total of 16 gene neighbors in modules 40, 72
Gene neighbors (16)
Gene Common Name Description Module membership
DVU0375 Glu/Leu/Phe/Val dehydrogenase family protein 72, 130
DVU0860 None 59, 72
DVU0889 phosphonopyruvate decarboxylase-like protein 59, 72
DVU1115 hypothetical protein DVU1115 72, 101
DVU1122 portal protein 21, 40
DVU1123 hypothetical protein DVU1123 40, 101
DVU1124 hypothetical protein DVU1124 40, 101
DVU1733 hypothetical protein DVU1733 72, 243
DVU1740 hypothetical protein DVU1740 72, 253
DVU2158 hypothetical protein DVU2158 3, 72
DVU2611 hypothetical protein DVU2611 40, 72
DVU2695 hypothetical protein DVU2695 40, 72
DVU2704 hypothetical protein DVU2704 40, 168
DVU2713 hypothetical protein DVU2713 40, 276
DVU2740 livF high-affinity branched-chain amino acid ABC transporter ATP-binding protein 72, 264
DVUA0011 nifK nitrogenase molybdenum-iron protein subunit beta 47, 72
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 DVU2695
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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