Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2827

sigma-54 dependent transcriptional regulator

CircVis
Functional Annotations (10)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2827
(Mouseover regulator name to see its description)

DVU2827 is regulated by 22 influences and regulates 14 modules.
Regulators for DVU2827 (22)
Regulator Module Operator
DVU0539 170 tf
DVU0916 170 tf
DVU1572 170 tf
DVU1572
DVU2106
170 combiner
DVU1628 170 tf
DVU1645
DVU3313
170 combiner
DVU2114 170 tf
DVU2675 170 tf
DVU2956 170 tf
DVU3080 170 tf
DVU3313 170 tf
DVU3313
DVU2106
170 combiner
DVU2106 339 tf
DVU2106
DVU2835
339 combiner
DVU2423 339 tf
DVU2527 339 tf
DVU2527
DVU1584
339 combiner
DVU2644
DVU1584
339 combiner
DVU2686
DVU1584
339 combiner
DVU2836 339 tf
DVU3080 339 tf
DVU3255
DVU2644
339 combiner

Warning: DVU2827 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
325 0.00e+00 aAaaatTca.aatcttctTccAat
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RegPredict
326 2.70e-05 AaATCAtaaaaAaAtTcCAAACAG
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RegPredict
643 6.00e-06 cAA.aaaa.Ttaaaa
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RegPredict
644 1.90e-01 atTTtgttgtgtTgA
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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 DVU2827

DVU2827 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Transcriptional regulator containing PAS, AAA-type ATPase, and DNA-binding domains cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
signal transducer activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
signal transduction go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
sensory_box tigr/ tigrfam
Module neighborhood information for DVU2827

DVU2827 has total of 42 gene neighbors in modules 170, 339
Gene neighbors (42)
Gene Common Name Description Module membership
DVU0163 lipoprotein 170, 279
DVU0369 hypothetical protein DVU0369 170, 263
DVU0371 hypothetical protein DVU0371 190, 339
DVU0554 NAD-dependent epimerase/dehydratase family protein 190, 339
DVU0555 hypothetical protein DVU0555 190, 339
DVU0556 ISDvu3, transposase OrfA 190, 339
DVU0557 None 190, 339
DVU0558 hypothetical protein DVU0558 190, 339
DVU0559 None 190, 339
DVU0561 glycosyl transferase group 1 family protein 190, 339
DVU0562 ISD1, transposase OrfA 190, 339
DVU0604 hypothetical protein DVU0604 170, 283
DVU0923 L-PSP family endoribonuclease 283, 339
DVU1010 hypothetical protein DVU1010 170, 179
DVU1015 hypothetical protein DVU1015 8, 170
DVU1147 alginate o-acetyltransferase AlgI 190, 339
DVU1155 hypothetical protein DVU1155 8, 170
DVU1166 hypothetical protein DVU1166 190, 339
DVU1167 hypothetical protein DVU1167 190, 339
DVU1277 hypothetical protein DVU1277 170, 339
DVU1478 hypothetical protein DVU1478 170, 233
DVU1637 hypothetical protein DVU1637 8, 170
DVU1638 hypothetical protein DVU1638 8, 170
DVU1639 hypothetical protein DVU1639 8, 170
DVU1760 TetR family transcriptional regulator 170, 279
DVU1832 hypothetical protein DVU1832 332, 339
DVU1905 hypothetical protein DVU1905 170, 279
DVU1964 Rrf2 family transcriptional regulator 170, 219
DVU1965 hypothetical protein DVU1965 170, 219
DVU2010 ISD1, transposase OrfB 190, 339
DVU2048 hypothetical protein DVU2048 337, 339
DVU2145 chloramphenicol acetyltransferase 8, 170
DVU2146 hypothetical protein DVU2146 8, 170
DVU2175 adenine specific DNA methyltransferase 190, 339
DVU2182 hypothetical protein DVU2182 170, 263
DVU2183 hypothetical protein DVU2183 170, 263
DVU2229 motA-2 chemotaxis protein MotA 78, 170
DVU2415 hypothetical protein DVU2415 143, 170
DVU2827 sigma-54 dependent transcriptional regulator 170, 339
DVU2919 hypothetical protein DVU2919 170, 219
DVU3089 hypothetical protein DVU3089 143, 339
DVU3328 hypothetical protein DVU3328 143, 170
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 DVU2827
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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