Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3367 aspS
aspartyl-tRNA synthetase
Functional Annotations (8)
Function | System |
---|---|
Aspartyl-tRNA synthetase | cog/ cog |
nucleic acid binding | go/ molecular_function |
aspartate-tRNA ligase activity | go/ molecular_function |
ATP binding | go/ molecular_function |
cytoplasm | go/ cellular_component |
aspartyl-tRNA aminoacylation | go/ biological_process |
Aminoacyl-tRNA biosynthesis | kegg/ kegg pathway |
aspS_bact | tigr/ tigrfam |
Regulation information for DVU3367
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0682 DVU2275 |
188 | combiner |
DVU1547 DVU0230 |
188 | combiner |
DVU1547 DVU3142 |
188 | combiner |
DVU1547 DVUA0024 |
188 | combiner |
DVU1561 | 188 | tf |
DVU2275 | 188 | tf |
DVU2532 DVU2275 |
188 | combiner |
DVU2547 | 188 | tf |
DVU2547 DVU2195 |
188 | combiner |
DVU2547 DVU2832 |
188 | combiner |
DVU3167 DVU2582 |
188 | combiner |
DVU1561 DVU0118 |
113 | combiner |
DVU2547 | 113 | tf |
DVU2547 DVU1419 |
113 | combiner |
DVU2547 DVU2394 |
113 | combiner |
DVU2557 DVU2195 |
113 | combiner |
DVU2557 DVU2547 |
113 | combiner |
DVU2577 DVU0118 |
113 | combiner |
DVU3167 | 113 | tf |
DVU3167 DVU0063 |
113 | combiner |
DVU3167 DVU1584 |
113 | combiner |
DVU3220 | 113 | tf |
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 |
---|---|---|---|---|
217 | 6.80e+01 | TTTGcCataT | RegPredict | |
218 | 7.50e+04 | atAtCgtagccGcgcgCCTTGC | RegPredict | |
359 | 3.00e+01 | CtTTtCcgaA | RegPredict | |
360 | 4.30e+04 | GCgtaccGCATcggGgCAtCcC | RegPredict |
Functional Enrichment for DVU3367
Function | System |
---|---|
Aspartyl-tRNA synthetase | cog/ cog |
nucleic acid binding | go/ molecular_function |
aspartate-tRNA ligase activity | go/ molecular_function |
ATP binding | go/ molecular_function |
cytoplasm | go/ cellular_component |
aspartyl-tRNA aminoacylation | go/ biological_process |
Aminoacyl-tRNA biosynthesis | kegg/ kegg pathway |
aspS_bact | tigr/ tigrfam |
Module neighborhood information for DVU3367
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0113 | hisI | phosphoribosyl-AMP cyclohydrolase | 113, 230 |
DVU0114 | hisG | ATP phosphoribosyltransferase | 113, 228 |
DVU0274 | hypothetical protein DVU0274 | 188, 236 | |
DVU0387 | His/Glu/Gln/Arg/opine ABC transporter permease | 113, 288 | |
DVU0794 | fabI | enoyl-ACP reductase | 9, 113 |
DVU0796 | hisD | histidinol dehydrogenase | 113, 223 |
DVU0836 | trmD | tRNA (guanine-N1)-methyltransferase | 188, 306 |
DVU0840 | ffh | signal recognition particle protein | 28, 188 |
DVU0885 | amidohydrolase family protein | 30, 113 | |
DVU0950 | hypothetical protein DVU0950 | 160, 188 | |
DVU0957 | rpsR | 30S ribosomal protein S18 | 10, 188 |
DVU0958 | rplI | 50S ribosomal protein L9 | 186, 188 |
DVU0959 | dnaB | replicative DNA helicase | 186, 188 |
DVU1021 | hypothetical protein DVU1021 | 186, 188 | |
DVU1022 | SUF system FeS assembly ATPase SufC | 186, 188 | |
DVU1042 | tatB | twin-arginine translocation protein TatB | 64, 113 |
DVU1282 | glmM | phosphoglucosamine mutase | 52, 188 |
DVU1455 | hypothetical protein DVU1455 | 137, 188 | |
DVU1624 | kdsA | 2-dehydro-3-deoxyphosphooctonate aldolase | 188, 292 |
DVU1625 | YrbI family phosphatase | 188, 292 | |
DVU1627 | ABC transporter ATP-binding protein | 188, 330 | |
DVU1635 | hypothetical protein DVU1635 | 174, 188 | |
DVU1764 | hypothetical protein DVU1764 | 113, 261 | |
DVU1841 | fbp | fructose-1,6-bisphosphatase | 64, 188 |
DVU1863 | flagellar synthesis regulator FleN | 9, 113 | |
DVU1950 | indolepyruvate ferredoxin oxidoreductase subunit beta | 30, 113 | |
DVU1952 | hypothetical protein DVU1952 | 28, 113 | |
DVU2051 | hypothetical protein DVU2051 | 113, 163 | |
DVU2054 | hypothetical protein DVU2054 | 30, 113 | |
DVU2252 | dnaA-2 | chromosomal replication initiator protein DnaA | 188, 206 |
DVU2275 | sigma-54 dependent transcriptional regulator | 113, 195 | |
DVU2522 | hypothetical protein DVU2522 | 113, 188 | |
DVU2552 | gltX | glutamyl-tRNA synthetase | 113, 223 |
DVU2903 | HD domain-containing protein | 27, 188 | |
DVU2910 | hypothetical protein DVU2910 | 69, 113 | |
DVU2916 | hemK | hemK protein | 113, 278 |
DVU2917 | lpxC | UDP-3-O- | 113, 219 |
DVU2921 | rpmG | 50S ribosomal protein L33 | 186, 188 |
DVU3070 | hypothetical protein DVU3070 | 163, 188 | |
DVU3071 | oxidoreductase | 186, 188 | |
DVU3207 | RNB-like family protein | 188, 278 | |
DVU3274 | hypothetical protein DVU3274 | 55, 188 | |
DVU3367 | aspS | aspartyl-tRNA synthetase | 113, 188 |
DVU3368 | hisS | histidyl-tRNA synthetase | 10, 113 |
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.
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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;- 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.