Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2014

metallo-beta-lactamase family protein

CircVis
Functional Annotations (4)
Function System
Uncharacterized flavoproteins cog/ cog
FMN binding go/ molecular_function
oxidoreductase activity go/ molecular_function
hydrolase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2014
(Mouseover regulator name to see its description)

DVU2014 is regulated by 13 influences and regulates 0 modules.
Regulators for DVU2014 (13)
Regulator Module Operator
DVU0110 229 tf
DVU0110
DVU1144
229 combiner
DVU1331
DVU0110
229 combiner
DVU1517 229 tf
DVU1572
DVU2547
229 combiner
DVU3313
DVU0110
229 combiner
DVU1063 53 tf
DVU1402 53 tf
DVU1584
DVU1419
53 combiner
DVU2527 53 tf
DVU2835
DVU1744
53 combiner
DVU2953
DVU1402
53 combiner
DVUA0143
DVU3066
53 combiner

Warning: DVU2014 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
103 2.90e-01 ATaa..aAAaTtAat.TttGa
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RegPredict
104 4.40e+01 gCAgcctaCAcaGgGacAg
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RegPredict
437 3.40e+01 GTaTgttcGTGGTAtgaTGa
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RegPredict
438 2.90e+02 ccATaTcCgTTgaCttgcgTg
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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 DVU2014

DVU2014 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Uncharacterized flavoproteins cog/ cog
FMN binding go/ molecular_function
oxidoreductase activity go/ molecular_function
hydrolase activity go/ molecular_function
Module neighborhood information for DVU2014

DVU2014 has total of 57 gene neighbors in modules 53, 229
Gene neighbors (57)
Gene Common Name Description Module membership
DVU0146 hypothetical protein DVU0146 53, 119
DVU0147 lipoprotein 37, 53
DVU0148 lipoprotein 53, 99
DVU0149 hypothetical protein DVU0149 53, 99
DVU0150 hypothetical protein DVU0150 53, 99
DVU0152 phosphoenolpyruvate synthase-like protein 53, 99
DVU0322 eno phosphopyruvate hydratase 229, 236
DVU0372 hypothetical protein DVU0372 53, 214
DVU0407 rare lipoprotein A family protein 16, 229
DVU0458 hypothetical protein DVU0458 53, 313
DVU0593 L-lysine exporter 53, 247
DVU0594 iciA chromosome replication initiation inhibitor protein 17, 53
DVU0627 ptB phosphotransbutyrylase 192, 229
DVU0678 hypothetical protein DVU0678 53, 247
DVU0682 DNA-binding protein 141, 229
DVU0751 His/Glu/Gln/Arg/opine ABC transporter permease 53, 292
DVU0790 radical SAM family protein 134, 229
DVU0805 hypothetical protein DVU0805 53, 296
DVU0806 chemotaxis protein CheY 53, 296
DVU0882 hypothetical protein DVU0882 53, 60
DVU1405 hypothetical protein DVU1405 229, 308
DVU1670 hypothetical protein DVU1670 53, 62
DVU1780 hypothetical protein DVU1780 169, 229
DVU1781 hypothetical protein DVU1781 169, 229
DVU1782 iron-sulfur cluster-binding protein 169, 229
DVU1783 hypothetical protein DVU1783 169, 229
DVU1784 short chain dehydrogenase/reductase family oxidoreductase 169, 229
DVU1785 MarC membrane protein 169, 229
DVU1862 GGDEF domain-containing protein 94, 229
DVU1901 peptidyl-prolyl cis-trans isomerase domain-containing protein 12, 229
DVU1916 hypothetical protein DVU1916 229, 245
DVU1921 hynB-1 periplasmic 229, 348
DVU1922 hynA-1 periplasmic 229, 348
DVU1923 hupD hydrogenase expression/formation protein HupD 229, 308
DVU1924 hypC hydrogenase assembly chaperone HypC/HupF 109, 229
DVU1925 GDSL family lipase 109, 229
DVU2013 hydroxylamine reductase 27, 229
DVU2014 metallo-beta-lactamase family protein 53, 229
DVU2021 hypothetical protein DVU2021 229, 273
DVU2061 pfkA diphosphate--fructose-6-phosphate 1-phosphotransferase 53, 313
DVU2088 hypothetical protein DVU2088 33, 53
DVU2104 iron-sulfur cluster-binding/ATPase 53, 308
DVU2353 glycosyl transferase group 2 family protein 50, 229
DVU2416 hypothetical protein DVU2416 229, 268
DVU2460 hypothetical protein DVU2460 229, 236
DVU2675 LuxR family transcriptional regulator 229, 279
DVU2770 response regulator 71, 229
DVU2937 TPR domain/response regulator receiver domain-containing protein 71, 229
DVU2952 hypothetical protein DVU2952 53, 122
DVU3035 methyl-accepting chemotaxis protein 137, 229
DVU3049 hemerythrin family protein 35, 229
DVU3125 lipoprotein 53, 122
DVU3182 dcrA methyl-accepting chemotaxis protein DcrA 53, 343
DVU3188 NLP/P60 family protein 53, 216
DVU3384 zraP zinc resistance-associated protein 53, 247
DVUA0036 TPR domain-containing protein 53, 247
DVUA0061 hypothetical protein DVUA0061 53, 150
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 DVU2014
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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