Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2989 pspF

psp operon transcriptional activator

CircVis
Functional Annotations (8)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
phageshock_pspF tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2989
(Mouseover regulator name to see its description)

DVU2989 is regulated by 21 influences and regulates 21 modules.
Regulators for DVU2989 pspF (21)
Regulator Module Operator
DVU0230 31 tf
DVU0653 31 tf
DVU0653
DVU2114
31 combiner
DVU0682
DVU0653
31 combiner
DVU1561
DVU0539
31 combiner
DVU2036
DVU2114
31 combiner
DVU2423
DVU3142
31 combiner
DVU3142 31 tf
DVU3255
DVU1690
31 combiner
DVUA0151
DVU1561
31 combiner
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: DVU2989 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
61 0.00e+00 atgt.tAtTttTTt....ttgtA
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RegPredict
62 1.20e-01 cCaTgTtgTtaaAaaAacCAcaAA
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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 DVU2989

DVU2989 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
phageshock_pspF tigr/ tigrfam
Module neighborhood information for DVU2989

DVU2989 has total of 45 gene neighbors in modules 13, 31
Gene neighbors (45)
Gene Common Name Description Module membership
DVU0025 sensory box histidine kinase 31, 281
DVU0109 sensor histidine kinase 31, 311
DVU0139 sensor histidine kinase 31, 97
DVU0294 glycosyl transferase group 2 family protein 31, 105
DVU0317 hypothetical protein DVU0317 31, 286
DVU0445 CBS domain-containing protein 31, 299
DVU0447 hypothetical protein DVU0447 13, 19
DVU0527 maF Maf-like protein 13, 270
DVU0578 formate dehydrogenase accessory protein FdhD 31, 281
DVU0717 GGDEF domain/EAL domain-containing protein 31, 283
DVU0759 M29 family peptidase 13, 227
DVU1079 trmE tRNA modification GTPase TrmE 31, 82
DVU1083 phoB phosphate regulon transcriptional regulator PhoB 13, 97
DVU1228 tpX thiol peroxidase 31, 216
DVU1230 hypothetical protein DVU1230 31, 256
DVU1231 amt ammonium transporter 31, 256
DVU1232 glnB-1 nitrogen regulatory protein P-II 31, 215
DVU1295 sat sulfate adenylyltransferase 31, 74
DVU1466 argB acetylglutamate kinase 13, 57
DVU1488 minor tail protein 13, 338
DVU1534 hypothetical protein DVU1534 31, 175
DVU1535 hypothetical protein DVU1535 31, 105
DVU1563 sensory box histidine kinase/response regulator 31, 324
DVU1654 phage integrase family site specific recombinase 31, 86
DVU1729 killer protein 13, 90
DVU1731 hypothetical protein DVU1731 31, 267
DVU1821 hypothetical protein DVU1821 13, 289
DVU1822 glutamate synthase, amidotransferase subunit 13, 289
DVU1823 glutamate synthase, iron-sulfur cluster-binding subunit 13, 289
DVU1872 hypothetical protein DVU1872 31, 100
DVU2040 hypothetical protein DVU2040 31, 273
DVU2116 pilin 13, 85
DVU2268 hypothetical protein DVU2268 31, 261
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
DVU3132 glycerol-3-phosphate dehydrogenase, FAD-dependent 31, 203
DVU3269 sensory box histidine kinase/response regulator 31, 281
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
DVU3385 hypothetical protein DVU3385 31, 103
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 DVU2989
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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