Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3180

GGDEF domain-containing protein

CircVis
Functional Annotations (8)
Function System
Predicted signal transduction protein cog/ cog
signal transducer activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
cyclic nucleotide biosynthetic process go/ biological_process
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
GGDEF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3180
(Mouseover regulator name to see its description)

DVU3180 is regulated by 19 influences and regulates 0 modules.
Regulators for DVU3180 (19)
Regulator Module Operator
DVU1517
DVU0539
33 combiner
DVU1754
DVU2111
33 combiner
DVU2036
DVU2097
33 combiner
DVU2036
DVU2633
33 combiner
DVU2788
DVU2114
33 combiner
DVU2909
DVU1517
33 combiner
DVU3142 33 tf
DVUA0024 33 tf
DVUA0143 33 tf
DVU0277 87 tf
DVU0436 87 tf
DVU0436
DVU0529
87 combiner
DVU0529
DVU1083
87 combiner
DVU0653 87 tf
DVU1517 87 tf
DVU2195
DVU0529
87 combiner
DVU2785
DVU0230
87 combiner
DVUA0024 87 tf
DVUA0057 87 tf

Warning: DVU3180 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
65 5.10e+02 aTaGgAtAtTTcTT
Loader icon
RegPredict
66 2.30e+02 tTGtCctttagctTggggtGTgt
Loader icon
RegPredict
171 1.70e-04 GggcttC.GCaaCg
Loader icon
RegPredict
172 7.10e+02 ttTcgctGTGcTgCGgtGcgCt
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 DVU3180

DVU3180 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Predicted signal transduction protein cog/ cog
signal transducer activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
cyclic nucleotide biosynthetic process go/ biological_process
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
GGDEF tigr/ tigrfam
Module neighborhood information for DVU3180

DVU3180 has total of 57 gene neighbors in modules 33, 87
Gene neighbors (57)
Gene Common Name Description Module membership
DVU0077 hypothetical protein DVU0077 87, 162
DVU0126 ABC transporter ATP-binding protein 33, 181
DVU0258 sensory box histidine kinase/response regulator 83, 87
DVU0295 amine oxidase, flavin-containing 87, 162
DVU0541 lipoprotein 33, 285
DVU0661 dihydrouridine synthase family protein 87, 185
DVU0731 hypothetical protein DVU0731 87, 126
DVU0740 hypothetical protein DVU0740 87, 162
DVU0742 hypothetical protein DVU0742 83, 87
DVU0743 sensory box histidine kinase 14, 87
DVU0802 hypothetical protein DVU0802 33, 121
DVU0973 4-hydroxybenzoate octaprenyltransferase 33, 83
DVU0993 hypothetical protein DVU0993 33, 121
DVU1056 cobalt ABC transporter ATP-binding protein 33, 327
DVU1150 hypothetical protein DVU1150 33, 334
DVU1172 hypothetical protein DVU1172 33, 174
DVU1173 mviN-1 integral membrane protein MviN 33, 181
DVU1187 hypothetical protein DVU1187 87, 176
DVU1280 hypothetical protein DVU1280 33, 330
DVU1347 M24/M37 family peptidase 33, 327
DVU1357 hypothetical protein DVU1357 75, 87
DVU1371 HAD family hydrolase 87, 126
DVU1391 hypothetical protein DVU1391 69, 87
DVU1435 hypothetical protein DVU1435 69, 87
DVU1439 hypothetical protein DVU1439 87, 155
DVU1465 CgeB family protein 87, 334
DVU1744 DNA-binding protein 33, 181
DVU1762 hypothetical protein DVU1762 33, 343
DVU1857 methyl-accepting chemotaxis protein 33, 122
DVU1869 methyl-accepting chemotaxis protein 87, 122
DVU1908 pdxJ pyridoxine 5'-phosphate synthase 33, 150
DVU1934 phosphonate ABC transporter permease 33, 262
DVU2060 hypothetical protein DVU2060 33, 71
DVU2087 hypothetical protein DVU2087 33, 196
DVU2088 hypothetical protein DVU2088 33, 53
DVU2306 phosphate transporter family protein 33, 154
DVU2447 hypothetical protein DVU2447 33, 81
DVU2627 hypothetical protein DVU2627 14, 33
DVU2700 hypothetical protein DVU2700 33, 69
DVU2885 iron-containing alcohol dehydrogenase 87, 334
DVU2949 hypothetical protein DVU2949 33, 334
DVU2993 glycosyl transferase group 1/2 family protein 83, 87
DVU2996 NAD-dependent epimerase/dehydratase family protein 87, 150
DVU2997 hypothetical protein DVU2997 87, 150
DVU2998 hypothetical protein DVU2998 87, 150
DVU3008 NeuB family protein 87, 176
DVU3015 hypothetical protein DVU3015 83, 87
DVU3017 hypothetical protein DVU3017 69, 87
DVU3038 hypothetical protein DVU3038 33, 121
DVU3039 hypothetical protein DVU3039 33, 343
DVU3115 hypothetical protein DVU3115 33, 334
DVU3126 None 87, 150
DVU3175 hypothetical protein DVU3175 33, 327
DVU3180 GGDEF domain-containing protein 33, 87
DVU3196 twin-arginine translocation pathway signal sequence domain-containing protein 87, 214
DVU3215 response regulator 87, 250
DVU3224 sfsA sugar fermentation stimulation protein 83, 87
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 DVU3180
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