Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3179 ispB

octaprenyl-diphosphate synthase

CircVis
Functional Annotations (4)
Function System
Geranylgeranyl pyrophosphate synthase cog/ cog
isoprenoid biosynthetic process go/ biological_process
Terpenoid backbone biosynthesis kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3179
(Mouseover regulator name to see its description)

DVU3179 is regulated by 24 influences and regulates 0 modules.
Regulators for DVU3179 ispB (24)
Regulator Module Operator
DVU0110 172 tf
DVU0230 172 tf
DVU0653 172 tf
DVU0813 172 tf
DVU1518
DVU1730
172 combiner
DVU1674 172 tf
DVU1674
DVU0525
172 combiner
DVU1788 172 tf
DVU2086 172 tf
DVU2359
DVU2690
172 combiner
DVU0030
DVUA0057
174 combiner
DVU0057
DVU0230
174 combiner
DVU0594
DVU0653
174 combiner
DVU0606
DVU0653
174 combiner
DVU0653
DVU0679
174 combiner
DVU0653
DVU2251
174 combiner
DVU0813
DVU0230
174 combiner
DVU2423
DVU2832
174 combiner
DVU2588
DVU0813
174 combiner
DVU2588
DVU1964
174 combiner
DVU3167 174 tf
DVU3313
DVU2588
174 combiner
DVUA0024 174 tf
DVUA0057 174 tf

Warning: DVU3179 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
329 1.30e-02 aGCaTaCaCccCcagAaCAggAca
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RegPredict
330 7.80e-01 TAcTtaaCaTCATttCtGtGATAA
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RegPredict
333 7.60e+03 GAagAaCt.gcCcaT
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RegPredict
334 9.10e+03 AcGaTACGGtaa.Gc.cgTC
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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 DVU3179

DVU3179 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Geranylgeranyl pyrophosphate synthase cog/ cog
isoprenoid biosynthetic process go/ biological_process
Terpenoid backbone biosynthesis kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for DVU3179

DVU3179 has total of 52 gene neighbors in modules 172, 174
Gene neighbors (52)
Gene Common Name Description Module membership
DVU0169 oligopeptide/dipeptide ABC transporter periplasmic oligopeptide/dipeptide-binding protein 174, 250
DVU0255 hypothetical protein DVU0255 172, 250
DVU0362 hypothetical protein DVU0362 174, 334
DVU0480 hypothetical protein DVU0480 174, 206
DVU0492 argC N-acetyl-gamma-glutamyl-phosphate reductase 172, 250
DVU0495 hypothetical protein DVU0495 172, 180
DVU0569 sigma-54 dependent transcriptional regulator 162, 174
DVU0654 U32 family peptidase 172, 174
DVU0697 mannose-1-phosphate guanylyltransferase/mannose-6-phosphate isomerase 172, 296
DVU0876 metallo-beta-lactamase family protein 145, 172
DVU0897 RNA modification protein 172, 304
DVU0898 hypothetical protein DVU0898 172, 304
DVU0899 hypothetical protein DVU0899 146, 172
DVU0900 gmk guanylate kinase 172, 304
DVU0911 truA tRNA pseudouridine synthase A 30, 174
DVU1000 M24 family peptidase 172, 296
DVU1001 coenzyme A binding protein 52, 172
DVU1002 hypothetical protein DVU1002 169, 172
DVU1003 dnaJ domain-containing protein 169, 172
DVU1172 hypothetical protein DVU1172 33, 174
DVU1182 hypothetical protein DVU1182 26, 172
DVU1266 hypothetical protein DVU1266 172, 337
DVU1268 hypothetical protein DVU1268 82, 172
DVU1269 hypothetical protein DVU1269 69, 172
DVU1271 general secretion pathway protein F 174, 221
DVU1353 dnaE DNA polymerase III subunit alpha 65, 172
DVU1635 hypothetical protein DVU1635 174, 188
DVU1914 alpha-isopropylmalate/homocitrate synthase family transferase 172, 196
DVU1961 cheW-3 chemotaxis protein CheW 174, 286
DVU2144 gap-2 glyceraldehyde 3-phosphate dehydrogenase 54, 174
DVU2322 UTP--glucose-1-phosphate uridylyltransferase 23, 174
DVU2368 fabZ (3R)-hydroxymyristoyl-ACP dehydratase 52, 174
DVU2369 lpxD UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase 174, 251
DVU2576 oligopeptide ABC transporter ATP-binding protein 174, 318
DVU2674 succinate dehydrogenase and fumarate reductase iron-sulfur protein 172, 318
DVU2677 sensor histidine kinase/response regulator 166, 172
DVU2693 hypothetical protein DVU2693 174, 330
DVU2905 iron-containing alcohol dehydrogenase 83, 174
DVU3013 glycosyl transferase group 2 family protein 162, 174
DVU3022 sensory box histidine kinase/response regulator 162, 174
DVU3046 glycosyl transferase group 1 family protein 174, 206
DVU3048 asd aspartate-semialdehyde dehydrogenase 35, 172
DVU3050 hypothetical protein DVU3050 174, 278
DVU3109 iron-sulfur cluster-binding protein 174, 278
DVU3156 glmS glucosamine--fructose-6-phosphate aminotransferase (isomerizing) 172, 321
DVU3163 ABC transporter permease 174, 251
DVU3164 ABC transporter permease 174, 336
DVU3178 hypothetical protein DVU3178 172, 292
DVU3179 ispB octaprenyl-diphosphate synthase 172, 174
DVU3181 purL phosphoribosylformylglycinamidine synthase II 81, 174
DVU3192 glycosyl transferase group 1 family protein 172, 176
DVU3379 ribonucleotide-diphosphate reductase subunit alpha 172, 195
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 DVU3179
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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