Organism : Desulfovibrio vulgaris Hildenborough
| Module List :
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DVU2258 ruvC
Holliday junction resolvase
Functional Annotations (8)
Function | System |
---|---|
Holliday junction resolvasome, endonuclease subunit | cog/ cog |
nucleic acid binding | go/ molecular_function |
DNA repair | go/ biological_process |
DNA recombination | go/ biological_process |
crossover junction endodeoxyribonuclease activity | go/ molecular_function |
lipoate-protein ligase activity | go/ molecular_function |
Homologous recombination | kegg/ kegg pathway |
ruvC | tigr/ tigrfam |
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Regulation information for DVU2258
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0813 DVU0230 |
119 | combiner |
DVU0813 DVU1517 |
119 | combiner |
DVU1572 DVU0269 |
119 | combiner |
DVU1572 DVU3255 |
119 | combiner |
DVU1788 | 119 | tf |
DVU2675 DVU3186 |
119 | combiner |
DVU2909 DVU1788 |
119 | combiner |
DVU3255 DVU1584 |
119 | combiner |
DVU1628 DVU1964 |
65 | combiner |
DVU1949 | 65 | tf |
DVU2675 | 65 | tf |
DVU2788 DVU0629 |
65 | combiner |
DVU2788 DVU2557 |
65 | combiner |
DVU2788 DVU3186 |
65 | combiner |
DVU2799 DVU1628 |
65 | combiner |
DVU2799 DVU2394 |
65 | combiner |
DVU3313 | 65 | 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 |
---|---|---|---|---|
127 | 8.30e+00 | GaatCGgCatCgtAtgacA |
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RegPredict |
128 | 3.70e+00 | cATgcgGgAtGTtcCgcCggcag |
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RegPredict |
229 | 1.60e+03 | CTgCTTGcaCggcA.gGctCGC |
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RegPredict |
230 | 1.30e+04 | ATCATACATAcAA |
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RegPredict |
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Functional Enrichment for DVU2258
Function | System |
---|---|
Holliday junction resolvasome, endonuclease subunit | cog/ cog |
nucleic acid binding | go/ molecular_function |
DNA repair | go/ biological_process |
DNA recombination | go/ biological_process |
crossover junction endodeoxyribonuclease activity | go/ molecular_function |
lipoate-protein ligase activity | go/ molecular_function |
Homologous recombination | kegg/ kegg pathway |
ruvC | tigr/ tigrfam |
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Module neighborhood information for DVU2258
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0093 | glycosyl transferase domain-containing protein | 119, 289 | |
DVU0146 | hypothetical protein DVU0146 | 53, 119 | |
DVU0159 | thioesterase family protein | 57, 119 | |
DVU0160 | carbohydrate isomerase KpsF/GutQ family protein | 57, 119 | |
DVU0182 | radical SAM domain-containing protein | 65, 254 | |
DVU0243 | lipoprotein | 57, 119 | |
DVU0286 | hisF | imidazole glycerol phosphate synthase subunit HisF | 15, 65 |
DVU0319 | NAD-dependent epimerase/dehydratase | 62, 119 | |
DVU0333 | hypothetical protein DVU0333 | 65, 137 | |
DVU0359 | HesB-like domain-containing protein | 119, 226 | |
DVU0380 | sulfatase | 119, 305 | |
DVU0417 | speA | arginine decarboxylase | 57, 119 |
DVU0418 | lys1 | saccharopine dehydrogenase | 119, 236 |
DVU0703 | lepA | GTP-binding protein LepA | 28, 65 |
DVU0831 | PTS system transporter subunit IID | 64, 119 | |
DVU0868 | cdsA | phosphatidate cytidylyltransferase | 28, 65 |
DVU0871 | pyrH | uridylate kinase | 28, 65 |
DVU0988 | carbohydrate kinase | 23, 65 | |
DVU0990 | endonuclease III | 23, 65 | |
DVU0991 | hypothetical protein DVU0991 | 23, 65 | |
DVU1054 | HAD superfamily hydrolase | 65, 230 | |
DVU1071 | hypothetical protein DVU1071 | 65, 261 | |
DVU1192 | acylphosphatase | 66, 119 | |
DVU1196 | leuS | leucyl-tRNA synthetase | 65, 169 |
DVU1197 | nusB | N utilization substance protein B | 65, 248 |
DVU1214 | dolichyl-phosphate-mannose-protein mannosyltransferase family protein | 65, 294 | |
DVU1215 | PAP2 family protein | 65, 278 | |
DVU1251 | hypothetical protein DVU1251 | 65, 270 | |
DVU1272 | general secretion pathway protein E | 65, 221 | |
DVU1273 | type II/III secretion system protein | 65, 270 | |
DVU1275 | hypothetical protein DVU1275 | 65, 221 | |
DVU1352 | 6-pyruvoyl tetrahydrobiopterin synthase | 65, 291 | |
DVU1353 | dnaE | DNA polymerase III subunit alpha | 65, 172 |
DVU1395 | C4-type zinc finger DksA/TraR family protein | 65, 254 | |
DVU1467 | hslU | ATP-dependent protease ATP-binding subunit HslU | 119, 227 |
DVU1599 | crcB | crcB protein | 65, 337 |
DVU1621 | hypothetical protein DVU1621 | 28, 65 | |
DVU1722 | hypothetical protein DVU1722 | 119, 167 | |
DVU1878 | ltaE | threonine aldolase | 65, 270 |
DVU1879 | glycosyl transferase group 1 family protein | 65, 270 | |
DVU1907 | ugd | UDP-glucose 6-dehydrogenase | 65, 251 |
DVU2135 | hypothetical protein DVU2135 | 65, 208 | |
DVU2224 | hypothetical protein DVU2224 | 65, 86 | |
DVU2258 | ruvC | Holliday junction resolvase | 65, 119 |
DVU2420 | hypothetical protein DVU2420 | 119, 236 | |
DVU2486 | acetyltransferase | 119, 167 | |
DVU2554 | hypothetical protein DVU2554 | 119, 227 | |
DVU2555 | MATE efflux family protein | 119, 120 | |
DVU2641 | lipoprotein | 119, 254 | |
DVU2658 | hypothetical protein DVU2658 | 119, 215 | |
DVU2659 | exsB protein | 119, 215 | |
DVU2667 | phosphate ABC transporter periplasmic phosphate-binding protein | 119, 137 | |
DVU2752 | rhodanese-like domain-containing protein | 97, 119 | |
DVU2876 | terminase large subunit | 7, 119 | |
DVU3066 | DNA-binding protein | 65, 270 |
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.
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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.
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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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.