Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3335
sensory box histidine kinase
Functional Annotations (8)
Function | System |
---|---|
Signal transduction histidine kinase | cog/ cog |
two-component sensor activity | go/ molecular_function |
ATP binding | go/ molecular_function |
regulation of transcription, DNA-dependent | go/ biological_process |
signal transduction | go/ biological_process |
membrane | go/ cellular_component |
peptidyl-histidine phosphorylation | go/ biological_process |
sensory_box | tigr/ tigrfam |
Regulation information for DVU3335
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0118 DVU2251 |
249 | combiner |
DVU0230 | 249 | tf |
DVU0230 DVU2989 |
249 | combiner |
DVU0653 DVU2251 |
249 | combiner |
DVU0854 DVU2251 |
249 | combiner |
DVU2686 DVU0118 |
249 | combiner |
DVU2989 | 249 | tf |
DVU3220 DVU2251 |
249 | combiner |
DVU1517 | 162 | tf |
DVU2588 DVU0529 |
162 | combiner |
DVU2785 DVU0230 |
162 | combiner |
DVU3255 DVU0110 |
162 | combiner |
DVUA0057 DVU0529 |
162 | combiner |
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 |
---|---|---|---|---|
309 | 8.80e+01 | CG.aagaCatgACA | RegPredict | |
310 | 3.60e+03 | CTgCc.gATGg | RegPredict | |
475 | 3.20e+01 | cttcgc..t.tgtctTG.Cgc | RegPredict | |
476 | 1.00e+04 | TtgtTaTttTc.AgAaGTtT | RegPredict |
Functional Enrichment for DVU3335
Function | System |
---|---|
Signal transduction histidine kinase | cog/ cog |
two-component sensor activity | go/ molecular_function |
ATP binding | go/ molecular_function |
regulation of transcription, DNA-dependent | go/ biological_process |
signal transduction | go/ biological_process |
membrane | go/ cellular_component |
peptidyl-histidine phosphorylation | go/ biological_process |
sensory_box | tigr/ tigrfam |
Module neighborhood information for DVU3335
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0029 | hydantoinase/oxoprolinase family protein | 162, 185 | |
DVU0071 | dinP | DNA polymerase IV | 161, 162 |
DVU0077 | hypothetical protein DVU0077 | 87, 162 | |
DVU0080 | fumC | fumarate hydratase | 14, 162 |
DVU0104 | cation ABC transporter permease | 69, 162 | |
DVU0121 | hypothetical protein DVU0121 | 206, 249 | |
DVU0127 | hypothetical protein DVU0127 | 162, 316 | |
DVU0154 | hypothetical protein DVU0154 | 162, 334 | |
DVU0184 | hypothetical protein DVU0184 | 162, 337 | |
DVU0194 | terminase large subunit | 162, 334 | |
DVU0291 | ABC transporter ATP-binding protein | 35, 162 | |
DVU0292 | hypothetical protein DVU0292 | 162, 185 | |
DVU0295 | amine oxidase, flavin-containing | 87, 162 | |
DVU0346 | hypothetical protein DVU0346 | 162, 181 | |
DVU0347 | hexapaptide repeat-containing transferase | 55, 162 | |
DVU0521 | csrA | carbon storage regulator | 184, 249 |
DVU0540 | sensor histidine kinase | 162, 198 | |
DVU0569 | sigma-54 dependent transcriptional regulator | 162, 174 | |
DVU0585 | hypothetical protein DVU0585 | 126, 162 | |
DVU0740 | hypothetical protein DVU0740 | 87, 162 | |
DVU0844 | None | 126, 162 | |
DVU0859 | hypothetical protein DVU0859 | 69, 162 | |
DVU0907 | hypothetical protein DVU0907 | 162, 277 | |
DVU1051 | ccmE | cytochrome c-type biogenesis protein CcmE | 14, 249 |
DVU1283 | galU | UTP-glucose-1-phosphate uridylyltransferase | 60, 249 |
DVU1372 | hypothetical protein DVU1372 | 232, 249 | |
DVU1373 | divIVA | cell-division initiation protein DivIVA | 232, 249 |
DVU1374 | hypothetical protein DVU1374 | 232, 249 | |
DVU1375 | hypothetical protein DVU1375 | 232, 249 | |
DVU1377 | ilvH | acetolactate synthase 3 regulatory subunit | 232, 249 |
DVU1378 | ilvC | ketol-acid reductoisomerase | 232, 249 |
DVU1389 | hypothetical protein DVU1389 | 69, 162 | |
DVU1881 | phoH family protein | 12, 249 | |
DVU1882 | HDIG domain-containing protein | 95, 249 | |
DVU1883 | hypothetical protein DVU1883 | 117, 249 | |
DVU1887 | hypothetical protein DVU1887 | 128, 249 | |
DVU1910 | YjeF-like protein | 146, 249 | |
DVU2315 | hypothetical protein DVU2315 | 162, 176 | |
DVU2328 | hydrogenase nickel insertion protein HypA | 145, 249 | |
DVU2430 | RNA-binding protein | 249, 296 | |
DVU2508 | murF | UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase | 249, 301 |
DVU2509 | murE | UDP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligase | 249, 301 |
DVU2514 | pyk | pyruvate kinase | 249, 348 |
DVU2612 | hypothetical protein DVU2612 | 63, 249 | |
DVU2619 | hypothetical protein DVU2619 | 145, 162 | |
DVU2866 | hypothetical protein DVU2866 | 162, 204 | |
DVU2867 | holin | 162, 204 | |
DVU2883 | selA | selenocysteine synthase | 62, 162 |
DVU2970 | acetyltransferase | 162, 285 | |
DVU3013 | glycosyl transferase group 2 family protein | 162, 174 | |
DVU3022 | sensory box histidine kinase/response regulator | 162, 174 | |
DVU3045 | sensory box histidine kinase/response regulator | 11, 249 | |
DVU3097 | outer membrane efflux protein | 141, 249 | |
DVU3112 | hypothetical protein | 249, 315 | |
DVU3113 | carA | carbamoyl phosphate synthase small subunit | 14, 249 |
DVU3197 | ilvE | branched-chain amino acid aminotransferase | 220, 249 |
DVU3335 | sensory box histidine kinase | 162, 249 |
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.
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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;- 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
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