Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2690

hypothetical protein DVU2690

CircVis
Functional Annotations (1)
Function System
iron ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2690
(Mouseover regulator name to see its description)

DVU2690 is regulated by 25 influences and regulates 58 modules.
Regulators for DVU2690 (25)
Regulator Module Operator
DVU0230
DVU0621
182 combiner
DVU0539 182 tf
DVU0596
DVU2832
182 combiner
DVU0653
DVU2251
182 combiner
DVU1517 182 tf
DVU1754 182 tf
DVU1967
DVU0539
182 combiner
DVU2802
DVU2832
182 combiner
DVU2832 182 tf
DVU3080 182 tf
DVU3255
DVU2527
182 combiner
DVU0230 39 tf
DVU0525 39 tf
DVU0653
DVU2251
39 combiner
DVU1083
DVU2832
39 combiner
DVU1517 39 tf
DVU1518 39 tf
DVU1518
DVU0539
39 combiner
DVU2567 39 tf
DVU2785
DVU2832
39 combiner
DVU2832 39 tf
DVU3142 39 tf
DVU3255
DVU0653
39 combiner
DVUA0024
DVU0529
39 combiner
DVUA0057
DVU0529
39 combiner

Warning: DVU2690 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
77 1.70e+03 AaTCtTAAttA
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RegPredict
78 3.00e+03 AaaA.cctGAaCaCTcta.T
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RegPredict
347 1.20e+02 cTCatgCCcccGCa
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RegPredict
348 3.30e+03 cTCTTGCa
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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 DVU2690

DVU2690 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
iron ion binding go/ molecular_function
Module neighborhood information for DVU2690

DVU2690 has total of 22 gene neighbors in modules 39, 182
Gene neighbors (22)
Gene Common Name Description Module membership
DVU0008 hypothetical protein DVU0008 39, 284
DVU0010 TRAP transporter subunit DctQ 182, 238
DVU0039 C4-type zinc finger DksA/TraR family protein 182, 213
DVU1112 hypothetical protein DVU1112 2, 182
DVU1164 amiF formamidase 39, 276
DVU1713 hypothetical protein DVU1713 182, 213
DVU1754 hypothetical protein DVU1754 39, 47
DVU1967 Rrf2 family transcriptional regulator 39, 299
DVU1968 oxidoreductase 39, 299
DVU2191 hypothetical protein DVU2191 39, 259
DVU2194 hypothetical protein DVU2194 39, 259
DVU2278 hypothetical protein DVU2278 39, 47
DVU2480 hypothetical protein DVU2480 39, 149
DVU2688 bacteriophage transposase A protein 182, 231
DVU2689 bacteriophage DNA transposition B protein 182, 213
DVU2690 hypothetical protein DVU2690 39, 182
DVU2691 hypothetical protein DVU2691 39, 182
DVU2692 hypothetical protein DVU2692 182, 197
DVU2710 hypothetical protein DVU2710 182, 276
DVU2714 hypothetical protein DVU2714 182, 231
DVU2715 hypothetical protein DVU2715 182, 276
DVU3370 hypothetical protein DVU3370 182, 264
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 DVU2690
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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