Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1959

EAL/GGDEF domain-containing protein

CircVis
Functional Annotations (5)
Function System
FOG: EAL 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 DVU1959
(Mouseover regulator name to see its description)

DVU1959 is regulated by 17 influences and regulates 0 modules.
Regulators for DVU1959 (17)
Regulator Module Operator
DVU0057
DVU0230
313 combiner
DVU0230 313 tf
DVU0529 313 tf
DVU0653
DVU1063
313 combiner
DVU1674 313 tf
DVU2802
DVU2832
313 combiner
DVU3111
DVU2690
313 combiner
DVU0525 144 tf
DVU0653
DVU2251
144 combiner
DVU0813
DVU2832
144 combiner
DVU0936 144 tf
DVU1754
DVU2111
144 combiner
DVU1967 144 tf
DVU2686 144 tf
DVU3111
DVU2832
144 combiner
DVU3193
DVU2251
144 combiner
DVUA0024 144 tf

Warning: DVU1959 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
275 1.90e+00 ggCAgGgCATcgtCaa.acca
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RegPredict
276 2.80e+03 AatccGgATaCCCaCACCa
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RegPredict
597 1.90e+02 tCCtTcTTCt
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RegPredict
598 1.30e+02 ACCtTGCC.tC
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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 DVU1959

DVU1959 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
FOG: EAL 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 DVU1959

DVU1959 has total of 43 gene neighbors in modules 144, 313
Gene neighbors (43)
Gene Common Name Description Module membership
DVU0013 sensory box histidine kinase 239, 313
DVU0134 glycosyl transferase group 2 family protein 144, 185
DVU0228 hypothetical protein DVU0228 225, 313
DVU0287 None 239, 313
DVU0427 hypothetical protein DVU0427 144, 313
DVU0458 hypothetical protein DVU0458 53, 313
DVU0747 ABC transporter ATP-binding protein 106, 144
DVU0861 glycosyl transferase group 1 family protein 144, 208
DVU0962 hypothetical protein DVU0962 144, 225
DVU1157 sensory box histidine kinase 144, 305
DVU1158 hypothetical protein DVU1158 144, 305
DVU1163 major facilitator superfamily protein 15, 144
DVU1250 gidB methyltransferase GidB 64, 313
DVU1256 heptosyltransferase family protein 179, 313
DVU1485 hypothetical protein DVU1485 134, 313
DVU1545 hemolysin-type calcium-binding repeat/calx-beta domain-containing protein 269, 313
DVU1697 hypothetical protein DVU1697 144, 265
DVU1727 hypothetical protein DVU1727 144, 265
DVU1732 hypothetical protein DVU1732 134, 313
DVU1743 hypothetical protein DVU1743 84, 313
DVU1856 hypothetical protein DVU1856 144, 261
DVU1906 hypothetical protein DVU1906 37, 313
DVU1959 EAL/GGDEF domain-containing protein 144, 313
DVU2061 pfkA diphosphate--fructose-6-phosphate 1-phosphotransferase 53, 313
DVU2071 hypothetical protein DVU2071 144, 265
DVU2075 ParA family protein 77, 144
DVU2099 carbon monoxide dehydrogenase accessory protein CooC 68, 144
DVU2176 hypothetical protein DVU2176 283, 313
DVU2273 hypothetical protein DVU2273 144, 265
DVU2393 None 144, 260
DVU2528 hypothetical protein DVU2528 225, 313
DVU2565 bioD dethiobiotin synthetase 311, 313
DVU2654 hypothetical protein DVU2654 279, 313
DVU2685 hypothetical protein DVU2685 100, 313
DVU2737 RNA methyltransferase 144, 265
DVU2809 cytochrome c3 144, 305
DVU2811 formate dehydrogenase subunit beta 144, 305
DVU2826 hypothetical protein DVU2826 225, 313
DVU3311 hypothetical protein DVU3311 156, 313
DVU3318 hypothetical protein DVU3318 313, 320
DVU3322 hypothetical protein DVU3322 144, 222
DVU3323 ABC transporter permease 144, 222
DVU3324 ABC transporter ATP-binding protein 144, 222
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 DVU1959
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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