Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0379

transcriptional regulator

CircVis
Functional Annotations (3)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0379
(Mouseover regulator name to see its description)

DVU0379 is regulated by 15 influences and regulates 8 modules.
Regulators for DVU0379 (15)
Regulator Module Operator
DVU0653
DVU2251
305 combiner
DVU1754
DVU3305
305 combiner
DVU1967 305 tf
DVU1967
DVU0539
305 combiner
DVU2832 305 tf
DVU3186
DVU0653
305 combiner
DVU3305
DVU1967
305 combiner
DVU0653
DVU1744
51 combiner
DVU0936 51 tf
DVU0936
DVU2960
51 combiner
DVU1744 51 tf
DVU1754 51 tf
DVU1754
DVU2909
51 combiner
DVU2114
DVU1744
51 combiner
DVU2567 51 tf

Warning: DVU0379 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
99 7.20e+01 tGtTgccaaaGTTgcaGGc
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RegPredict
100 2.00e+04 CggGcCcgcAcAagG
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RegPredict
583 2.80e-02 cagctCatcg.caAaGccG
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RegPredict
584 7.30e+02 aAgaCCGgAtG
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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 DVU0379

DVU0379 is enriched for 3 functions in 3 categories.
Module neighborhood information for DVU0379

DVU0379 has total of 35 gene neighbors in modules 51, 305
Gene neighbors (35)
Gene Common Name Description Module membership
DVU0272 hypothetical protein DVU0272 51, 261
DVU0373 CoA-binding domain-containing protein 68, 305
DVU0374 pyruvate ferredoxin/flavodoxin oxidoreductase family protein 134, 305
DVU0376 hypothetical protein DVU0376 137, 305
DVU0377 trxB-1 thioredoxin reductase 25, 305
DVU0379 transcriptional regulator 51, 305
DVU0380 sulfatase 119, 305
DVU0393 ung uracil-DNA glycosylase 51, 211
DVU0568 tRNA 2-selenouridine synthase 51, 238
DVU0617 hypothetical protein DVU0617 160, 305
DVU0972 HD domain-containing protein 51, 84
DVU1104 baseplate assembly protein 305, 322
DVU1157 sensory box histidine kinase 144, 305
DVU1158 hypothetical protein DVU1158 144, 305
DVU1216 hypothetical protein DVU1216 238, 305
DVU1284 priA primosomal protein n' 254, 305
DVU1546 hypothetical protein DVU1546 51, 68
DVU1667 FtsK/SpoIIIE family protein 51, 261
DVU1983 hypothetical protein DVU1983 25, 51
DVU2303 hypothetical protein DVU2303 51, 284
DVU2440 hypothetical protein DVU2440 66, 305
DVU2466 flocculin repeat-containing protein 51, 261
DVU2492 trpF-2 N-(5'-phosphoribosyl)anthranilate isomerase 116, 305
DVU2642 alanyl-tRNA synthetase family protein 254, 305
DVU2809 cytochrome c3 144, 305
DVU2810 formate dehydrogenase formation protein FdhE 225, 305
DVU2811 formate dehydrogenase subunit beta 144, 305
DVU2812 fdnG-3 formate dehydrogenase subunit alpha, selenocysteine-containing 67, 305
DVU3063 mviN-2 integral membrane protein MviN 238, 305
DVU3160 hypothetical protein DVU3160 67, 305
DVU3189 NOL1/NOP2/sun family protein 51, 84
DVU3236 hflX GTP-binding protein HflX 51, 82
DVU3241 hypothetical protein DVU3241 160, 305
DVU3390 None 106, 305
DVU3391 hypothetical protein DVU3391 37, 305
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 DVU0379
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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