Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVUA0100

sigma-54 dependent transcriptional regulator

CircVis
Functional Annotations (9)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component signal transduction system (phosphorelay) go/ biological_process
nucleotide binding go/ molecular_function
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
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVUA0100
(Mouseover regulator name to see its description)

DVUA0100 is regulated by 18 influences and regulates 21 modules.
Regulators for DVUA0100 (18)
Regulator Module Operator
DVU0030 136 tf
DVU0621
DVU1744
136 combiner
DVU1628 136 tf
DVU1674
DVU2086
136 combiner
DVU1674
DVU3186
136 combiner
DVU2114 136 tf
DVU2527
DVU2114
136 combiner
DVU2577
DVU3095
136 combiner
DVU0621
DVU1744
131 combiner
DVU1628 131 tf
DVU1674
DVU0629
131 combiner
DVU2114 131 tf
DVU2114
DVUA0143
131 combiner
DVU2527
DVU1144
131 combiner
DVU2527
DVU2251
131 combiner
DVU2577
DVU2114
131 combiner
DVU2799 131 tf
DVU3095 131 tf

Warning: DVUA0100 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
253 3.20e+01 GcAcAgtgtGCtcaCGTAtCaCaC
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RegPredict
254 4.50e+00 CGc.gcG.GCctagTcGcGcC
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RegPredict
263 1.00e+01 CATGaAgagaGgagAaaac
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RegPredict
264 2.40e+03 GaaGaggtcAtacgc
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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 DVUA0100

DVUA0100 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component signal transduction system (phosphorelay) go/ biological_process
nucleotide binding go/ molecular_function
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
Module neighborhood information for DVUA0100

DVUA0100 has total of 36 gene neighbors in modules 131, 136
Gene neighbors (36)
Gene Common Name Description Module membership
DVU0490 None 60, 136
DVUA0027 hypothetical protein DVUA0027 131, 175
DVUA0030 hypothetical protein DVUA0030 131, 213
DVUA0032 hypothetical protein DVUA0032 136, 197
DVUA0033 hypothetical protein DVUA0033 136, 314
DVUA0079 cysC adenylylsulfate kinase 131, 136
DVUA0081 glycosyl transferase, group 1/2 family protein 131, 136
DVUA0086 response regulator 131, 211
DVUA0099 HAMP domain-containing protein 131, 136
DVUA0100 sigma-54 dependent transcriptional regulator 131, 136
DVUA0101 hrpY/hrcU family type III secretion protein 131, 136
DVUA0102 escT type III secretion inner membrane protein 131, 197
DVUA0103 invX HrpO family type III secretion protein 131, 334
DVUA0104 type III secretion inner membrane protein HrcV family 131, 136
DVUA0106 YopN family type III secretion target protein 25, 131
DVUA0107 hypothetical protein DVUA0107 131, 136
DVUA0108 hypothetical protein DVUA0108 131, 136
DVUA0109 LcrH/SycD family type III secretion system chaperone 131, 136
DVUA0111 type III secretion system protein IpaC family 136, 195
DVUA0112 type III secretion system protein YscC family 136, 150
DVUA0113 YscD family type III secretion protein 131, 136
DVUA0114 hypothetical protein DVUA0114 136, 211
DVUA0115 type III secretion system protein YscF family 131, 136
DVUA0116 hypothetical protein DVUA0116 131, 136
DVUA0117 escJ type III secretion lipoprotein 136, 211
DVUA0119 type III secretion system ATPase 136, 150
DVUA0121 type III secretion system protein YopQ family 131, 136
DVUA0122 type III secretion system protein 131, 136
DVUA0123 anti-anti-sigma factor 131, 136
DVUA0124 sigma factor serine-protein kinase 136, 150
DVUA0126 hypothetical protein DVUA0126 131, 136
DVUA0128 hypothetical protein DVUA0128 131, 197
DVUA0131 CRISPR-associated Csd1 family protein 131, 136
DVUA0132 CRISPR-associated Csh2 family protein 131, 150
DVUA0147 hypothetical protein DVUA0147 131, 136
DVUA0149 hypothetical protein DVUA0149 61, 136
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 DVUA0100
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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