Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVUA0127

None

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVUA0127
(Mouseover regulator name to see its description)

DVUA0127 is regulated by 18 influences and regulates 0 modules.
Regulators for DVUA0127 (18)
Regulator Module Operator
DVU0813 167 tf
DVU0946
DVU0269
167 combiner
DVU1584 167 tf
DVU1628
DVU0813
167 combiner
DVU1949 167 tf
DVU2086
DVU0744
167 combiner
DVU2275
DVU0269
167 combiner
DVU2547 167 tf
DVU2547
DVU0230
167 combiner
DVU3381 167 tf
DVU0525 265 tf
DVU0653
DVU2251
265 combiner
DVU1754 265 tf
DVU1754
DVU2097
265 combiner
DVU2114 265 tf
DVU2686 265 tf
DVU2832 265 tf
DVU3229
DVU2832
265 combiner

Warning: DVUA0127 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
319 1.10e-04 ATcaATTcAcaAAGaCaGGAGCCG
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RegPredict
320 4.40e-02 CTCCACGgccatcatccGcAA
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RegPredict
505 1.30e+02 cGgctgCggCA..a
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RegPredict
506 4.00e+04 AAGAAAGA
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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 DVUA0127

Warning: No Functional annotations were found!

Module neighborhood information for DVUA0127

DVUA0127 has total of 38 gene neighbors in modules 167, 265
Gene neighbors (38)
Gene Common Name Description Module membership
DVU0131 hypothetical protein DVU0131 167, 222
DVU0132 hypothetical protein DVU0132 167, 222
DVU0133 hypothetical protein DVU0133 167, 222
DVU0254 hypothetical protein DVU0254 105, 167
DVU0401 hypothetical protein DVU0401 32, 167
DVU0587 fdnG-1 formate dehydrogenase subunit alpha, selenocysteine-containing 167, 274
DVU0684 hflK protein 167, 194
DVU0705 dctM TRAP transporter subunit DctM 92, 265
DVU1382 HesB family selenoprotein 167, 226
DVU1383 hypothetical protein DVU1383 57, 167
DVU1527 phage integrase family site specific recombinase 25, 265
DVU1697 hypothetical protein DVU1697 144, 265
DVU1722 hypothetical protein DVU1722 119, 167
DVU1726 hypothetical protein DVU1726 97, 265
DVU1727 hypothetical protein DVU1727 144, 265
DVU1838 trxB-2 thioredoxin-disulfide reductase 167, 222
DVU1839 trx thioredoxin 4, 167
DVU1943 hypothetical protein DVU1943 167, 226
DVU2044 hypothetical protein DVU2044 167, 196
DVU2064 2-nitropropane dioxygenase family oxidoreductase 208, 265
DVU2069 DNA processing protein DprA 208, 265
DVU2070 hypothetical protein 217, 265
DVU2071 hypothetical protein DVU2071 144, 265
DVU2137 sucCD succinyl-CoA synthase, beta/subunit alphas 106, 265
DVU2273 hypothetical protein DVU2273 144, 265
DVU2469 hypothetical protein DVU2469 4, 167
DVU2486 acetyltransferase 119, 167
DVU2489 hypothetical protein DVU2489 167, 194
DVU2593 hypothetical protein DVU2593 134, 265
DVU2737 RNA methyltransferase 144, 265
DVU2875 DNA-binding protein 134, 265
DVU2877 hypothetical protein DVU2877 265, 316
DVU2878 adenine specific DNA methyltransferase 265, 340
DVU2907 umuD umuD protein 134, 265
DVU3344 hypothetical protein DVU3344 167, 194
DVU3346 hypothetical protein DVU3346 120, 167
DVUA0029 hypothetical protein DVUA0029 167, 222
DVUA0127 None 167, 265
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 DVUA0127
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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