Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1414

sensory box protein

CircVis
Functional Annotations (9)
Function System
Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain cog/ cog
two-component sensor activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
cyclic nucleotide biosynthetic process go/ biological_process
membrane go/ cellular_component
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
sensory_box tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1414
(Mouseover regulator name to see its description)

DVU1414 is regulated by 16 influences and regulates 0 modules.
Regulators for DVU1414 (16)
Regulator Module Operator
DVU0653
DVU1690
299 combiner
DVU0653
DVU2251
299 combiner
DVU1517 299 tf
DVU1754 299 tf
DVU1754
DVU3334
299 combiner
DVU2690 299 tf
DVU2832 299 tf
DVUA0024 299 tf
DVUA0024
DVU0529
299 combiner
DVU1517 242 tf
DVU1517
DVU0539
242 combiner
DVU1754 242 tf
DVU1754
DVU3305
242 combiner
DVU2588
DVU1967
242 combiner
DVU3142 242 tf
DVU3255
DVU3186
242 combiner

Warning: DVU1414 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
461 0.00e+00 aa.TcTctGcAtaaGaaAaAtAat
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RegPredict
462 1.30e-03 ATTaccTCCaTCtCAcGGGaA
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RegPredict
573 4.50e+03 ATGtGgagTtTTtttt.GtTT
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RegPredict
574 6.80e+03 ACaAaATcagaAtaACa.tA
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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 DVU1414

DVU1414 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain cog/ cog
two-component sensor activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
cyclic nucleotide biosynthetic process go/ biological_process
membrane go/ cellular_component
phosphorus-oxygen lyase activity go/ molecular_function
intracellular signal transduction go/ biological_process
sensory_box tigr/ tigrfam
Module neighborhood information for DVU1414

DVU1414 has total of 32 gene neighbors in modules 242, 299
Gene neighbors (32)
Gene Common Name Description Module membership
DVU0185 hypothetical protein DVU0185 284, 299
DVU0442 phoH-like protein 299, 329
DVU0443 exonulcease 2, 299
DVU0445 CBS domain-containing protein 31, 299
DVU1105 hypothetical protein DVU1105 168, 299
DVU1162 hypothetical protein DVU1162 80, 242
DVU1414 sensory box protein 242, 299
DVU1503 terminase large subunit 152, 299
DVU1550 phosphoglycerate mutase family protein 242, 322
DVU1551 HD domain-containing protein 242, 322
DVU1552 hypothetical protein DVU1552 77, 242
DVU1553 AMP-binding protein 242, 322
DVU1554 radical SAM domain-containing protein 110, 242
DVU1555 hypothetical protein DVU1555 242, 322
DVU1556 hypothetical protein DVU1556 242, 322
DVU1557 hypothetical protein DVU1557 242, 322
DVU1558 hypothetical protein DVU1558 242, 322
DVU1559 mop aldehyde oxidoreductase 77, 242
DVU1560 molybdopterin biosynthesis protein 242, 322
DVU1561 molybdenum-binding protein 242, 263
DVU1721 hypothetical protein DVU1721 293, 299
DVU1753 hypothetical protein DVU1753 118, 242
DVU1967 Rrf2 family transcriptional regulator 39, 299
DVU1968 oxidoreductase 39, 299
DVU1969 hypothetical protein DVU1969 80, 299
DVU1970 response regulator 299, 322
DVU2168 major head protein 2, 299
DVU2171 portal protein 73, 299
DVU2173 hypothetical protein DVU2173 165, 299
DVU2187 hypothetical protein DVU2187 67, 299
DVU2773 hypothetical protein DVU2773 242, 326
DVU2774 hypothetical protein 208, 242
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 DVU1414
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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