Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2855

tail/DNA circulation protein

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

Cytoscape Web
Regulation information for DVU2855
(Mouseover regulator name to see its description)

DVU2855 is regulated by 21 influences and regulates 0 modules.
Regulators for DVU2855 (21)
Regulator Module Operator
DVU0230 341 tf
DVU0594 341 tf
DVU1949
DVU2251
341 combiner
DVU2644
DVU0063
341 combiner
DVU2644
DVU0653
341 combiner
DVU2644
DVU2106
341 combiner
DVU2644
DVU2251
341 combiner
DVU2644
DVU2527
341 combiner
DVU2827 341 tf
DVU2836 341 tf
DVUA0151 341 tf
DVU0230 314 tf
DVU0619
DVU0230
314 combiner
DVU0936 314 tf
DVU0936
DVU2275
314 combiner
DVU1547
DVU0230
314 combiner
DVU1572
DVU2527
314 combiner
DVU1674
DVU2532
314 combiner
DVU2251 314 tf
DVU2532 314 tf
DVUA0151 314 tf

Warning: DVU2855 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
599 3.40e-02 tCCGcTtcgGGCacGAcCGgaT
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RegPredict
600 1.30e+00 TCggcacCgTCgaCA
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RegPredict
647 1.10e+02 CcTtgCCtttGtCgt
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RegPredict
648 2.90e+04 cacacGcaacGcatGAcagtgCCC
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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 DVU2855

DVU2855 is enriched for 1 functions in 3 categories.
Enrichment Table (1)
Function System
Mu-like prophage DNA circulation protein cog/ cog
Module neighborhood information for DVU2855

DVU2855 has total of 56 gene neighbors in modules 314, 341
Gene neighbors (56)
Gene Common Name Description Module membership
DVU0009 TRAP transporter subunit DctM 181, 341
DVU0020 hypothetical protein DVU0020 99, 314
DVU0067 hypothetical protein DVU0067 181, 341
DVU0102 cation ABC transporter periplasmic binding protein 181, 341
DVU0189 P4 family phage/plasmid primase 204, 314
DVU0195 hypothetical protein DVU0195 222, 314
DVU0213 hypothetical protein DVU0213 161, 314
DVU0214 tail/DNA circulation protein 58, 314
DVU0216 phage baseplate assembly protein V 58, 314
DVU0217 tail protein 58, 314
DVU0218 tail protein 37, 314
DVU0219 tail protein 58, 314
DVU0220 tail fiber protein 148, 314
DVU0221 tail fiber assembly protein 198, 314
DVU0234 hypothetical protein DVU0234 281, 314
DVU0235 hypothetical protein DVU0235 281, 314
DVU0351 cytidine 5'monophosphate N-acetylneuraminic acid synthetase /polysaccharide biosynthesis protein 234, 341
DVU0381 nhaC-1 Na+/H+ antiporter NhaC 37, 341
DVU0448 gmd GDP-mannose 4,6-dehydratase 308, 341
DVU1035 glucokinase 234, 341
DVU1128 lysozyme 231, 341
DVU1129 hypothetical protein DVU1129 231, 341
DVU1239 hypothetical protein DVU1239 234, 341
DVU1446 heptosyltransferase family protein 318, 341
DVU1451 response regulator 318, 341
DVU1483 tail fiber assembly protein 134, 314
DVU1484 hypothetical protein DVU1484 134, 314
DVU1486 tail fiber protein, truncation 152, 314
DVU1508 hypothetical protein DVU1508 234, 341
DVU1810 hypothetical protein DVU1810 245, 341
DVU1858 cold shock domain-containing protein 234, 341
DVU2277 hypothetical protein DVU2277 261, 341
DVU2283 hypothetical protein DVU2283 234, 341
DVU2336 carboxyl-terminal protease 234, 341
DVU2457 hypothetical protein DVU2457 200, 314
DVU2733 adenine specific DNA methyltransferase 82, 314
DVU2848 tail fiber assembly protein 38, 314
DVU2849 tail fiber protein 247, 314
DVU2850 tail protein 58, 314
DVU2851 tail protein 58, 314
DVU2852 tail protein 38, 314
DVU2853 phage baseplate assembly protein V 58, 314
DVU2855 tail/DNA circulation protein 314, 341
DVU2856 hypothetical protein DVU2856 38, 314
DVU2871 minor capsid protein C 181, 341
DVU2874 hypothetical protein DVU2874 234, 341
DVU2992 glycosyl transferase group 2 family protein 222, 341
DVU3081 hypothetical protein DVU3081 181, 341
DVU3108 nhaC-2 Na+/H+ antiporter NhaC 181, 341
DVU3110 oxidoreductase 234, 341
DVU3267 hypothetical protein DVU3267 181, 341
DVU3325 hypothetical protein DVU3325 234, 341
DVUA0001 hypothetical protein DVUA0001 61, 314
DVUA0022 ABC transporter ATP-binding protein 61, 314
DVUA0033 hypothetical protein DVUA0033 136, 314
DVUA0096 major facilitator superfamily protein 234, 341
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 DVU2855
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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