Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3107

cytochrome c family protein

CircVis
Functional Annotations (4)
Function System
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3107
(Mouseover regulator name to see its description)

DVU3107 is regulated by 19 influences and regulates 0 modules.
Regulators for DVU3107 (19)
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
DVU0436 321 tf
DVU1561
DVU2588
321 combiner
DVU2275 321 tf
DVU2588
DVU0118
321 combiner
DVU2588
DVU0436
321 combiner
DVU2675
DVUA0024
321 combiner
DVU3186
DVU3023
321 combiner

Warning: DVU3107 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
Loader icon
RegPredict
22 3.70e+03 ATgAaaATAcT
Loader icon
RegPredict
611 1.20e-01 aatATCATgtC
Loader icon
RegPredict
612 1.90e+03 CagCAttgcagACG.cgcGaa
Loader icon
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 DVU3107

DVU3107 is enriched for 4 functions in 2 categories.
Enrichment Table (4)
Function System
iron ion binding go/ molecular_function
electron transport go/ biological_process
electron carrier activity go/ molecular_function
heme binding go/ molecular_function
Module neighborhood information for DVU3107

DVU3107 has total of 57 gene neighbors in modules 11, 321
Gene neighbors (57)
Gene Common Name Description Module membership
DVU0170 methyl-accepting chemotaxis protein 11, 241
DVU0330 response regulator 77, 321
DVU0331 sensory box histidine kinase 77, 321
DVU0591 methyl-accepting chemotaxis protein 77, 321
DVU0592 cheW-1 chemotaxis protein CheW 77, 321
DVU0700 methyl-accepting chemotaxis protein 77, 321
DVU0729 hypothetical protein DVU0729 11, 241
DVU0820 hypothetical protein DVU0820 11, 241
DVU0821 hypothetical protein DVU0821 11, 241
DVU0822 hypothetical protein DVU0822 11, 241
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
DVU1474 hypothetical protein DVU1474 239, 321
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
DVU1991 hypothetical protein DVU1991 175, 321
DVU2107 hypothetical protein DVU2107 11, 283
DVU2117 hypothetical protein DVU2117 11, 321
DVU2118 hypothetical protein DVU2118 77, 321
DVU2119 type II/III secretion system protein 77, 321
DVU2121 response regulator 77, 321
DVU2123 hypothetical protein DVU2123 161, 321
DVU2124 hypothetical protein DVU2124 161, 321
DVU2126 hypothetical protein DVU2126 77, 321
DVU2127 von Willebrand factor A 259, 321
DVU2264 hypothetical protein DVU2264 11, 279
DVU2281 sensor histidine kinase/response regulator 77, 321
DVU2304 hypothetical protein DVU2304 11, 241
DVU2345 hypothetical protein DVU2345 11, 241
DVU2410 sodB superoxide dismutase, Fe 105, 321
DVU2524 cytochrome c3 77, 321
DVU2526 hynA-2 periplasmic 77, 321
DVU2585 methyl-accepting chemotaxis protein 11, 241
DVU2615 solute-binding family 1 protein 11, 241
DVU2616 sensory box histidine kinase/response regulator 11, 148
DVU2626 hypothetical protein DVU2626 77, 321
DVU2676 hypothetical protein DVU2676 11, 241
DVU2679 sensory box histidine kinase/response regulator 68, 321
DVU2833 hypothetical protein DVU2833 11, 241
DVU3045 sensory box histidine kinase/response regulator 11, 249
DVU3062 sensor histidine kinase/response regulator 105, 321
DVU3107 cytochrome c family protein 11, 321
DVU3131 transcriptional regulator 92, 321
DVU3133 glycerol uptake facilitator protein 77, 321
DVU3134 glpK glycerol kinase 77, 321
DVU3143 iron-sulfur cluster-binding protein 138, 321
DVU3144 cytochrome c family protein 309, 321
DVU3155 dcrH methyl-accepting chemotaxis protein DcrH 11, 241
DVU3156 glmS glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 172, 321
DVU3246 RND efflux system outer membrane lipoprotein 77, 321
DVU3247 RND family efflux transporter MFP subunit 77, 321
DVU3248 AcrB/AcrD/AcrF family protein 295, 321
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 DVU3107
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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