Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3116 prfC

peptide chain release factor 3

CircVis
Functional Annotations (8)
Function System
Peptide chain release factor RF-3 cog/ cog
GTPase activity go/ molecular_function
GTP binding go/ molecular_function
cytoplasm go/ cellular_component
translational termination go/ biological_process
protein-synthesizing GTPase activity go/ molecular_function
translation release factor activity, codon specific go/ molecular_function
small_GTP tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3116
(Mouseover regulator name to see its description)

DVU3116 is regulated by 28 influences and regulates 0 modules.
Regulators for DVU3116 prfC (28)
Regulator Module Operator
DVU0063 235 tf
DVU0063
DVU1949
235 combiner
DVU0118 235 tf
DVU0118
DVU2690
235 combiner
DVU0682 235 tf
DVU0682
DVU1584
235 combiner
DVU1419 235 tf
DVU1572 235 tf
DVU1572
DVU2111
235 combiner
DVU2394 235 tf
DVU2547 235 tf
DVU0309
DVU0653
278 combiner
DVU0379
DVU0653
278 combiner
DVU0653 278 tf
DVU1063 278 tf
DVU1144 278 tf
DVU1419 278 tf
DVU1561
DVU2394
278 combiner
DVU1674
DVU1561
278 combiner
DVU1949 278 tf
DVU2195
DVU0629
278 combiner
DVU2275
DVU0569
278 combiner
DVU2547 278 tf
DVU2557 278 tf
DVU2557
DVU2195
278 combiner
DVU2686
DVU2195
278 combiner
DVU2909
DVU0569
278 combiner
DVU3167 278 tf

Warning: DVU3116 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
449 4.00e+02 ctcTTcCc.t
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RegPredict
450 1.40e+04 AAAAAG
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RegPredict
531 4.20e+04 cgtCCGaCtcctactttTtcag
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RegPredict
532 1.10e+05 AAAGACTT
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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 DVU3116

DVU3116 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Peptide chain release factor RF-3 cog/ cog
GTPase activity go/ molecular_function
GTP binding go/ molecular_function
cytoplasm go/ cellular_component
translational termination go/ biological_process
protein-synthesizing GTPase activity go/ molecular_function
translation release factor activity, codon specific go/ molecular_function
small_GTP tigr/ tigrfam
Module neighborhood information for DVU3116

DVU3116 has total of 53 gene neighbors in modules 235, 278
Gene neighbors (53)
Gene Common Name Description Module membership
DVU0135 hypothetical protein DVU0135 223, 278
DVU0399 hypothetical protein DVU0399 10, 235
DVU0450 ribF riboflavin biosynthesis protein RibF 75, 278
DVU0503 pnp polynucleotide phosphorylase/polyadenylase 10, 235
DVU0507 hypothetical protein DVU0507 10, 235
DVU0508 infB translation initiation factor IF-2 10, 235
DVU0510 nusA transcription elongation factor NusA 10, 235
DVU0660 phosphodiesterase 223, 278
DVU0723 purT phosphoribosylglycinamide formyltransferase 2 185, 278
DVU0724 sodium/alanine symporter family protein 223, 278
DVU0753 amino acid ABC transporter ATP-binding protein 235, 292
DVU0768 murI glutamate racemase 150, 278
DVU0769 pyridoxamine kinase 150, 278
DVU0808 gatA aspartyl/glutamyl-tRNA amidotransferase subunit A 28, 278
DVU0809 gatC glutamyl-tRNA(Gln) amidotransferase subunit C 29, 235
DVU0810 hypothetical protein DVU0810 29, 235
DVU0869 uppS undecaprenyl diphosphate synthase 28, 278
DVU1060 glycosyl transferase group 1 family protein 223, 278
DVU1215 PAP2 family protein 65, 278
DVU1247 hypothetical protein DVU1247 28, 235
DVU1248 argS arginyl-tRNA synthetase 29, 235
DVU1298 rpsL 30S ribosomal protein S12 10, 235
DVU1299 rpsG 30S ribosomal protein S7 10, 235
DVU1300 fusA-1 elongation factor G 10, 235
DVU1454 ispD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 5, 278
DVU1538 hypothetical protein DVU1538 28, 278
DVU1571 rho transcription termination factor Rho 5, 235
DVU1573 pth peptidyl-tRNA hydrolase 82, 278
DVU1622 purQ phosphoribosylformylglycinamidine synthase I 10, 235
DVU2209 hypothetical protein DVU2209 176, 278
DVU2216 infA translation initiation factor IF-1 235, 308
DVU2298 glycine/betaine/L-proline ABC transporter permease 94, 235
DVU2299 glycine/betaine/L-proline ABC transporter ATP binding protein 5, 235
DVU2436 hypothetical protein DVU2436 223, 278
DVU2581 response regulator 141, 278
DVU2756 radical SAM domain-containing protein 62, 278
DVU2872 lambda family phage portal protein 106, 278
DVU2902 pyrC dihydroorotase 141, 278
DVU2913 lipoprotein 10, 235
DVU2914 prfA peptide chain release factor 1 10, 235
DVU2916 hemK hemK protein 113, 278
DVU2945 hypothetical protein DVU2945 145, 278
DVU2995 glycosyl transferase group 1 family protein 150, 278
DVU3050 hypothetical protein DVU3050 174, 278
DVU3109 iron-sulfur cluster-binding protein 174, 278
DVU3116 prfC peptide chain release factor 3 235, 278
DVU3206 phosphoribosylaminoimidazolecarboxamide formyltransferase 5, 235
DVU3207 RNB-like family protein 188, 278
DVU3223 aspB aspartate aminotransferase 211, 278
DVU3307 ubiX 3-octaprenyl-4-hydroxybenzoate carboxy-lyase 29, 235
DVU3308 metallo-beta-lactamase family protein 10, 235
DVU3310 DEAD-box ATP dependent DNA helicase 10, 235
DVU3361 ADP-heptose synthase 211, 278
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 DVU3116
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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