Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1812

cytochrome c oxidase subunit II

CircVis
Functional Annotations (15)
Function System
Heme/copper-type cytochrome/quinol oxidases, subunit 2 cog/ cog
cytochrome-c oxidase activity go/ molecular_function
iron ion binding go/ molecular_function
copper ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
aa3-type cytochrome c oxidase go/ molecular_function
ba3-type cytochrome c oxidase go/ molecular_function
caa3-type cytochrome c oxidase go/ molecular_function
cbb3-type cytochrome c oxidase go/ molecular_function
integral to membrane go/ cellular_component
heme binding go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
CoxB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1812
(Mouseover regulator name to see its description)

DVU1812 is regulated by 25 influences and regulates 0 modules.
Regulators for DVU1812 (25)
Regulator Module Operator
DVU0030
DVU3080
11 combiner
DVU0309
DVU0063
11 combiner
DVU0309
DVU2111
11 combiner
DVU0309
DVU2989
11 combiner
DVU0309
DVU3334
11 combiner
DVU1561
DVU2114
11 combiner
DVU2114 11 tf
DVU2195
DVU0309
11 combiner
DVU2423 11 tf
DVU2557 11 tf
DVU2557
DVU2675
11 combiner
DVU3080 11 tf
DVU0309
DVU1788
148 combiner
DVU0309
DVU2989
148 combiner
DVU0629 148 tf
DVU0916 148 tf
DVU1561
DVU2114
148 combiner
DVU1788 148 tf
DVU2394
DVU0629
148 combiner
DVU2394
DVU1144
148 combiner
DVU2675 148 tf
DVU2675
DVU2394
148 combiner
DVU2989 148 tf
DVU3255
DVU2675
148 combiner
DVUA0151 148 tf

Warning: DVU1812 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
21 1.00e-01 ttTtcttGctaTaat
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RegPredict
22 3.70e+03 ATgAaaATAcT
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RegPredict
281 2.90e-02 ggtATGgTGccgca
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RegPredict
282 2.70e+00 CTCCtTGC
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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 DVU1812

DVU1812 is enriched for 15 functions in 3 categories.
Enrichment Table (15)
Function System
Heme/copper-type cytochrome/quinol oxidases, subunit 2 cog/ cog
cytochrome-c oxidase activity go/ molecular_function
iron ion binding go/ molecular_function
copper ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
aa3-type cytochrome c oxidase go/ molecular_function
ba3-type cytochrome c oxidase go/ molecular_function
caa3-type cytochrome c oxidase go/ molecular_function
cbb3-type cytochrome c oxidase go/ molecular_function
integral to membrane go/ cellular_component
heme binding go/ molecular_function
Oxidative phosphorylation kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
CoxB tigr/ tigrfam
Module neighborhood information for DVU1812

DVU1812 has total of 50 gene neighbors in modules 11, 148
Gene neighbors (50)
Gene Common Name Description Module membership
DVU0006 universal stress protein 132, 148
DVU0138 response regulator 132, 148
DVU0170 methyl-accepting chemotaxis protein 11, 241
DVU0174 hypothetical protein DVU0174 148, 241
DVU0220 tail fiber protein 148, 314
DVU0238 hypothetical protein DVU0238 132, 148
DVU0253 oxidoreductase 148, 153
DVU0278 glyoxalase family protein 148, 285
DVU0305 ferredoxin II 132, 148
DVU0729 hypothetical protein DVU0729 11, 241
DVU0820 hypothetical protein DVU0820 11, 241
DVU0821 hypothetical protein DVU0821 11, 241
DVU0822 hypothetical protein DVU0822 11, 241
DVU0883 glutaredoxin 60, 148
DVU0912 hypothetical protein DVU0912 11, 266
DVU0937 hypothetical protein DVU0937 11, 262
DVU1121 hypothetical protein DVU1121 11, 266
DVU1263 pppA type IV prepilin-like proteins leader peptidase 11, 241
DVU1568 ferritin 132, 148
DVU1569 porA pyruvate ferredoxin oxidoreductase subunit alpha 148, 153
DVU1773 hypothetical protein DVU1773 11, 121
DVU1774 hypothetical protein DVU1774 11, 241
DVU1811 protoheme IX farnesyltransferase 11, 241
DVU1812 cytochrome c oxidase subunit II 11, 148
DVU1816 hypothetical protein DVU1816 148, 153
DVU1904 cheW-2 chemotaxis protein CheW 132, 148
DVU2076 cheR-2 chemotaxis protein methyltransferase 132, 148
DVU2107 hypothetical protein DVU2107 11, 283
DVU2117 hypothetical protein DVU2117 11, 321
DVU2202 transglycosylase 132, 148
DVU2264 hypothetical protein DVU2264 11, 279
DVU2304 hypothetical protein DVU2304 11, 241
DVU2345 hypothetical protein DVU2345 11, 241
DVU2557 birA birA bifunctional protein 148, 348
DVU2583 lipoprotein 14, 148
DVU2585 methyl-accepting chemotaxis protein 11, 241
DVU2615 solute-binding family 1 protein 11, 241
DVU2616 sensory box histidine kinase/response regulator 11, 148
DVU2676 hypothetical protein DVU2676 11, 241
DVU2684 hypothetical protein DVU2684 71, 148
DVU2833 hypothetical protein DVU2833 11, 241
DVU2935 gpmA phosphoglyceromutase 71, 148
DVU2968 sensor histidine kinase/response regulator 148, 192
DVU3045 sensory box histidine kinase/response regulator 11, 249
DVU3107 cytochrome c family protein 11, 321
DVU3155 dcrH methyl-accepting chemotaxis protein DcrH 11, 241
DVU3227 flagellar basal body-associated protein 71, 148
DVU3263 frdB fumarate reductase iron-sulfur subunit 148, 348
DVU3296 hypothetical protein DVU3296 14, 148
DVUA0025 response regulator receiver domain-containing protein 11, 241
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 DVU1812
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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