Organism : Desulfovibrio vulgaris Hildenborough | Module List :
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0778
(Mouseover regulator name to see its description)

DVU0778 is regulated by 16 influences and regulates 0 modules.
Regulators for DVU0778 atpH (16)
Regulator Module Operator
DVU0057 346 tf
DVU0529 346 tf
DVU0596
DVU0057
346 combiner
DVU0619
DVU0230
346 combiner
DVU2532
DVU0946
346 combiner
DVU2788
DVU2532
346 combiner
DVU2802
DVU2909
346 combiner
DVU2909
DVU0529
346 combiner
DVUA0143 346 tf
DVU0744
DVU2690
319 combiner
DVU2275 319 tf
DVU2690 319 tf
DVU2802
DVU0057
319 combiner
DVU2802
DVU0539
319 combiner
DVU2802
DVU2588
319 combiner
DVU2802
DVU2799
319 combiner

Warning: DVU0778 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
607 1.10e-01 taAttcTGtTTgAgttggaGgacA
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RegPredict
608 1.20e+02 GgTgGTGaat
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RegPredict
657 1.80e-01 TtG.tatt...tTCACAA
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RegPredict
658 8.40e+02 ATTTTcTa
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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 DVU0778

Module neighborhood information for DVU0778

DVU0778 has total of 41 gene neighbors in modules 319, 346
Gene neighbors (41)
Gene Common Name Description Module membership
DVU0259 DNA-binding response regulator 343, 346
DVU0260 response regulator 346, 348
DVU0261 universal stress protein 296, 346
DVU0262 hypothetical protein DVU0262 296, 346
DVU0263 acidic cytochrome c3 346, 348
DVU0264 ferredoxin, 4Fe-4S 346, 348
DVU0265 hypothetical protein DVU0265 296, 346
DVU0266 hypothetical protein DVU0266 296, 346
DVU0267 hypothetical protein DVU0267 343, 346
DVU0269 Rrf2 family transcriptional regulator 179, 346
DVU0270 sensory box histidine kinase 277, 346
DVU0774 atpC F0F1 ATP synthase subunit epsilon 74, 319
DVU0775 atpD F0F1 ATP synthase subunit beta 74, 319
DVU0776 atpG F0F1 ATP synthase subunit gamma 74, 319
DVU0777 atpA F0F1 ATP synthase subunit alpha 74, 319
DVU0778 atpH F0F1 ATP synthase subunit delta 319, 346
DVU0779 ATP synthase F0 subunit B 74, 319
DVU0780 ATP synthase F0 subunit B' 74, 319
DVU0845 hypothetical protein DVU0845 74, 319
DVU0846 aprB adenylylsulphate reductase subunit beta 74, 319
DVU0847 aprA adenylylsulfate reductase subunit alpha 74, 319
DVU0848 heterodisulfide reductase 74, 319
DVU0849 heterodisulfide reductase, iron-sulfur-binding subunit 74, 319
DVU0850 heterodisulfide reductase, transmembrane subunit 74, 319
DVU0851 hypothetical protein DVU0851 74, 319
DVU0918 atpB ATP synthase F0 subunit A 74, 319
DVU1636 ppaC manganese-dependent inorganic pyrophosphatase 74, 319
DVU2287 hydrogenase subunit CooK 145, 346
DVU2290 hydrogenase subunit CooU 207, 346
DVU2292 hypA hydrogenase nickel insertion protein HypA 207, 346
DVU2293 cooF iron-sulfur protein CooF 207, 346
DVU2957 hypothetical protein DVU2957 285, 346
DVU2958 hypothetical protein DVU2958 285, 346
DVU2959 hypothetical protein DVU2959 285, 346
DVU2960 sigma-54 dependent transcriptional regulator 285, 346
DVU2962 sensor histidine kinase 285, 346
DVU2963 response regulator 285, 346
DVU2964 hypothetical protein DVU2964 285, 346
DVU2966 response regulator 285, 346
DVU2967 sensor histidine kinase/response regulator 285, 346
DVU3353 coaBC phosphopantothenoylcysteine decarboxylase/phosphopantothenate--cysteine ligase 50, 346
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 DVU0778
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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