Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1083 phoB

phosphate regulon transcriptional regulator PhoB

CircVis
Functional Annotations (6)
Function System
Response regulators consisting of a CheY-like receiver domain and a winged-helix DNA-binding domain cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1083
(Mouseover regulator name to see its description)

DVU1083 is regulated by 24 influences and regulates 19 modules.
Regulators for DVU1083 phoB (24)
Regulator Module Operator
DVU0539 97 tf
DVU0653 97 tf
DVU0679
DVU2832
97 combiner
DVU0916 97 tf
DVU1063 97 tf
DVU1517 97 tf
DVU1517
DVU0539
97 combiner
DVU1754
DVU2785
97 combiner
DVU2886
DVU1754
97 combiner
DVU3186 97 tf
DVU3193
DVU2114
97 combiner
DVU3255
DVU3186
97 combiner
DVUA0151 97 tf
DVU0525 13 tf
DVU0813 13 tf
DVU1517 13 tf
DVU2086
DVU2832
13 combiner
DVU2423 13 tf
DVU2832 13 tf
DVU3255
DVU0653
13 combiner
DVU3255
DVU0936
13 combiner
DVU3255
DVU2251
13 combiner
DVUA0151 13 tf
DVUA0151
DVU1730
13 combiner

Warning: DVU1083 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
25 3.90e-02 acaAgcGtgTGAaag.tTtC.ACA
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RegPredict
26 2.60e+00 tTacgtcacCatTtActgGTaAAa
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RegPredict
187 2.30e-02 AaCGAcgTgCaCcgc.CAaaAGA
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RegPredict
188 1.10e-01 GacAaagtgcAaCatc.ta..aac
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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 DVU1083

DVU1083 is enriched for 6 functions in 3 categories.
Module neighborhood information for DVU1083

DVU1083 has total of 41 gene neighbors in modules 13, 97
Gene neighbors (41)
Gene Common Name Description Module membership
DVU0078 hypothetical protein DVU0078 2, 97
DVU0139 sensor histidine kinase 31, 97
DVU0447 hypothetical protein DVU0447 13, 19
DVU0527 maF Maf-like protein 13, 270
DVU0622 sensor histidine kinase/response regulator 97, 311
DVU0759 M29 family peptidase 13, 227
DVU1083 phoB phosphate regulon transcriptional regulator PhoB 13, 97
DVU1156 sigma-54 dependent transcriptional regulator /response regulator 97, 345
DVU1224 nfo endonuclease IV 25, 97
DVU1466 argB acetylglutamate kinase 13, 57
DVU1488 minor tail protein 13, 338
DVU1726 hypothetical protein DVU1726 97, 265
DVU1729 killer protein 13, 90
DVU1821 hypothetical protein DVU1821 13, 289
DVU1822 glutamate synthase, amidotransferase subunit 13, 289
DVU1823 glutamate synthase, iron-sulfur cluster-binding subunit 13, 289
DVU2116 pilin 13, 85
DVU2269 hypothetical protein DVU2269 76, 97
DVU2270 hypothetical protein DVU2270 97, 118
DVU2271 pyruvate formate-lyase activating enzyme 97, 329
DVU2272 formate acetyltransferase 25, 97
DVU2665 phosphate ABC transporter permease 68, 97
DVU2736 hypothetical protein DVU2736 15, 97
DVU2750 cbiD cobalamin biosynthesis protein CbiD 68, 97
DVU2751 hypothetical protein DVU2751 97, 160
DVU2752 rhodanese-like domain-containing protein 97, 119
DVU2753 hypothetical protein 97, 326
DVU2939 hypothetical protein DVU2939 97, 326
DVU2986 pspC phage shock protein C 13, 156
DVU2987 hypothetical protein DVU2987 13, 156
DVU2988 pspA phage shock protein A 13, 156
DVU2989 pspF psp operon transcriptional activator 13, 31
DVU2990 moeA molybdopterin biosynthesis protein MoeA/LysR substrate binding-domain-containing protein 13, 123
DVU3170 cobJ precorrin-3b C17-methyltransferase 25, 97
DVU3336 potassium channel histidine kinase domain-containing protein/universal stress protein 13, 112
DVU3337 kdpC K+-transporting ATPase subunit C 13, 201
DVU3338 kdpB K+-transporting ATPase subunit B 13, 213
DVU3339 kdpA potassium-transporting ATPase subunit A 13, 213
DVUA0004 DNA-binding protein HU 68, 97
DVUA0066 patatin family phospholipase 38, 97
DVUA0093 chromate transport family protein 97, 197
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 DVU1083
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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