Organism : Desulfovibrio vulgaris Hildenborough
| Module List :
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DVU0911 truA
tRNA pseudouridine synthase A
Functional Annotations (6)
Function | System |
---|---|
Pseudouridylate synthase | cog/ cog |
pseudouridine synthesis | go/ biological_process |
RNA binding | go/ molecular_function |
pseudouridylate synthase activity | go/ molecular_function |
tRNA modification | go/ biological_process |
pseudouridine synthase activity | go/ molecular_function |
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Regulation information for DVU0911
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
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 |
DVU0629 | 30 | tf |
DVU1156 DVU0629 |
30 | combiner |
DVU1518 | 30 | tf |
DVU1561 DVU0629 |
30 | combiner |
DVU1949 | 30 | tf |
DVU2275 DVU1730 |
30 | combiner |
DVU2423 DVU2275 |
30 | combiner |
DVU3167 | 30 | tf |
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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 Id | e-value | Consensus | Motif Logo | RegPredict |
---|---|---|---|---|
59 | 1.90e-04 | CCTG.acaa.cAGggaG.GgaCtT |
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RegPredict |
60 | 6.70e+00 | aTCtaCCatCTTCaCaTTct |
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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 |
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Functional Enrichment for DVU0911
Function | System |
---|---|
Pseudouridylate synthase | cog/ cog |
pseudouridine synthesis | go/ biological_process |
RNA binding | go/ molecular_function |
pseudouridylate synthase activity | go/ molecular_function |
tRNA modification | go/ biological_process |
pseudouridine synthase activity | go/ molecular_function |
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Module neighborhood information for DVU0911
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0052 | era | GTP-binding protein Era | 5, 30 |
DVU0169 | oligopeptide/dipeptide ABC transporter periplasmic oligopeptide/dipeptide-binding protein | 174, 250 | |
DVU0176 | glycerophosphoryl diester phosphodiesterase family protein | 30, 316 | |
DVU0362 | hypothetical protein DVU0362 | 174, 334 | |
DVU0480 | hypothetical protein DVU0480 | 174, 206 | |
DVU0569 | sigma-54 dependent transcriptional regulator | 162, 174 | |
DVU0637 | hypothetical protein DVU0637 | 30, 103 | |
DVU0654 | U32 family peptidase | 172, 174 | |
DVU0730 | hypothetical protein DVU0730 | 30, 315 | |
DVU0885 | amidohydrolase family protein | 30, 113 | |
DVU0911 | truA | tRNA pseudouridine synthase A | 30, 174 |
DVU0930 | proB | gamma-glutamyl kinase | 30, 133 |
DVU0931 | thiD | phosphomethylpyrimidine kinase | 30, 306 |
DVU1009 | hypothetical protein DVU1009 | 5, 30 | |
DVU1172 | hypothetical protein DVU1172 | 33, 174 | |
DVU1178 | hypothetical protein DVU1178 | 30, 157 | |
DVU1271 | general secretion pathway protein F | 174, 221 | |
DVU1332 | selD | selenide, water dikinase, selenocysteine-containing | 30, 94 |
DVU1362 | hypothetical protein DVU1362 | 30, 277 | |
DVU1363 | rfbD | dTDP-4-dehydrorhamnose reductase | 30, 277 |
DVU1364 | rfbB | dTDP-glucose 4,6-dehydratase | 30, 277 |
DVU1365 | heme-binding protein | 30, 317 | |
DVU1366 | lipoprotein | 30, 277 | |
DVU1635 | hypothetical protein DVU1635 | 174, 188 | |
DVU1850 | CBS domain-containing protein | 16, 30 | |
DVU1950 | indolepyruvate ferredoxin oxidoreductase subunit beta | 30, 113 | |
DVU1961 | cheW-3 | chemotaxis protein CheW | 174, 286 |
DVU2052 | glycosyl transferase group 2 family protein | 30, 54 | |
DVU2053 | hypothetical protein DVU2053 | 30, 258 | |
DVU2054 | hypothetical protein DVU2054 | 30, 113 | |
DVU2055 | metG | methionyl-tRNA synthetase | 30, 223 |
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 |
DVU2464 | hypothetical protein DVU2464 | 23, 30 | |
DVU2576 | oligopeptide ABC transporter ATP-binding protein | 174, 318 | |
DVU2693 | hypothetical protein DVU2693 | 174, 330 | |
DVU2889 | BioY family protein | 30, 316 | |
DVU2896 | hypothetical protein | 30, 112 | |
DVU2905 | iron-containing alcohol dehydrogenase | 83, 174 | |
DVU2938 | hypothetical protein DVU2938 | 27, 30 | |
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 | |
DVU3050 | hypothetical protein DVU3050 | 174, 278 | |
DVU3109 | iron-sulfur cluster-binding protein | 174, 278 | |
DVU3163 | ABC transporter permease | 174, 251 | |
DVU3164 | ABC transporter permease | 174, 336 | |
DVU3179 | ispB | octaprenyl-diphosphate synthase | 172, 174 |
DVU3181 | purL | phosphoribosylformylglycinamidine synthase II | 81, 174 |
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.
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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.
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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.
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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;![](/static/images/help_images/circvis-help.png)
- 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
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