Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0940

GGDEF domain-containing protein

CircVis
Functional Annotations (5)
Function System
FOG: GGDEF domain cog/ cog
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 DVU0940
(Mouseover regulator name to see its description)

DVU0940 is regulated by 19 influences and regulates 0 modules.
Regulators for DVU0940 (19)
Regulator Module Operator
DVU0946 303 tf
DVU0946
DVU1144
303 combiner
DVU2114 303 tf
DVU2836
DVU3023
303 combiner
DVU3023 303 tf
DVU3167 303 tf
DVU3167
DVU2114
303 combiner
DVU3186 303 tf
DVU3186
DVU0110
303 combiner
DVU3193
DVU0946
303 combiner
DVU3255
DVU3186
303 combiner
DVU1063 214 tf
DVU1744 214 tf
DVU2785
DVU1517
214 combiner
DVU2785
DVU2195
214 combiner
DVU2953
DVU2960
214 combiner
DVU3023 214 tf
DVUA0024 214 tf
DVUA0057 214 tf

Warning: DVU0940 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
407 1.80e+02 Aac.caC.ACa.gAtAgGaA
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RegPredict
408 1.80e+01 CGCA.gAGGCATGAC
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RegPredict
579 1.30e-04 CA.gGTtTtttTacAgcaAtG
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RegPredict
580 3.60e+00 AAGATAAAATAACATCTTATTTAT
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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 DVU0940

DVU0940 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
FOG: GGDEF domain cog/ cog
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 DVU0940

DVU0940 has total of 44 gene neighbors in modules 214, 303
Gene neighbors (44)
Gene Common Name Description Module membership
DVU0229 hypothetical protein DVU0229 214, 296
DVU0297 hypothetical protein DVU0297 214, 334
DVU0372 hypothetical protein DVU0372 53, 214
DVU0405 cobB-1 cobyrinic acid a,c-diamide synthase 126, 214
DVU0546 hypothetical protein DVU0546 126, 214
DVU0620 L-PSP family endoribonuclease 63, 214
DVU0652 cheV-2 chemotaxis protein CheV 83, 214
DVU0656 hypothetical protein DVU0656 63, 303
DVU0657 HSP20 family protein 164, 303
DVU0666 HD domain-containing protein 214, 309
DVU0713 branched-chain amino acid ABC transporter permease 303, 347
DVU0940 GGDEF domain-containing protein 214, 303
DVU1376 ilvB-2 acetolactate synthase large subunit, biosynthetic type 117, 303
DVU1462 cytochrome c assembly protein 117, 303
DVU1464 heptosyltransferase family protein 117, 303
DVU1650 hypothetical protein DVU1650 300, 303
DVU1651 hypothetical protein DVU1651 128, 303
DVU1682 GAF domain-containing protein 163, 303
DVU1739 hypothetical protein DVU1739 121, 214
DVU1825 amidohydrolase family protein 27, 214
DVU1860 lnt apolipoprotein N-acyltransferase 9, 214
DVU1989 hypothetical protein DVU1989 214, 309
DVU2257 hypothetical protein DVU2257 9, 214
DVU2323 hypothetical protein DVU2323 164, 303
DVU2391 hypothetical protein DVU2391 198, 214
DVU2478 pstC phosphate ABC transporter permease PstC 126, 214
DVU2584 CorA family protein 126, 214
DVU2608 motA-3 flagellar motor protein MotA 88, 303
DVU2666 phosphate ABC transporter permease 99, 214
DVU2761 hypothetical protein DVU2761 181, 214
DVU2799 MarR family transcriptional regulator 272, 303
DVU2800 heavy metal translocating P-type ATPase 272, 303
DVU2801 hypothetical protein DVU2801 272, 303
DVU2825 pyruvate formate-lyase 1 activating enzyme 214, 222
DVU2843 DNA mismatch endonuclease Vsr 214, 334
DVU2844 hypothetical protein DVU2844 214, 334
DVU3023 sigma-54 dependent DNA-binding response regulator 23, 214
DVU3085 hypothetical protein DVU3085 88, 303
DVU3145 hydrogenase, b-type cytochrome subunit 214, 309
DVU3147 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 192, 214
DVU3195 lipoprotein 161, 214
DVU3196 twin-arginine translocation pathway signal sequence domain-containing protein 87, 214
DVU3261 frdC fumarate reductase, cytochrome subunit B 48, 303
DVU3356 NAD-dependent epimerase/dehydratase family protein 268, 303
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 DVU0940
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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