Organism : Desulfovibrio vulgaris Hildenborough
| Module List :
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DVU2413
radical SAM domain-containing protein
Functional Annotations (3)
Function | System |
---|---|
catalytic activity | go/ molecular_function |
iron-sulfur cluster binding | go/ molecular_function |
SAM_YgiQ | tigr/ tigrfam |
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Regulation information for DVU2413
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0110 | 185 | tf |
DVU0309 | 185 | tf |
DVU0309 DVU0946 |
185 | combiner |
DVU1144 | 185 | tf |
DVU1419 | 185 | tf |
DVU1517 | 185 | tf |
DVU1518 | 185 | tf |
DVU1518 DVU3080 |
185 | combiner |
DVU2114 DVU1063 |
185 | combiner |
DVU2319 | 185 | tf |
DVU2675 DVU1745 |
185 | combiner |
DVU2953 DVU1402 |
185 | combiner |
DVU0230 DVU1745 |
141 | combiner |
DVU0594 | 141 | tf |
DVU0653 | 141 | tf |
DVU0946 | 141 | tf |
DVU1517 | 141 | tf |
DVU1518 DVU1561 |
141 | combiner |
DVU2785 DVU0529 |
141 | combiner |
DVU2785 DVU1517 |
141 | combiner |
DVU2788 DVU0653 |
141 | combiner |
DVU3023 DVU2319 |
141 | combiner |
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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 |
---|---|---|---|---|
271 | 4.80e-03 | AatTAAAcAAAaGccGaGaaACaC |
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RegPredict |
272 | 4.50e+00 | GTatCgTgtgGgCtTgcgCcc |
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RegPredict |
353 | 6.90e-01 | GC.TCGcAACG |
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RegPredict |
354 | 7.30e+03 | CctTCCgGcAG |
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RegPredict |
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Functional Enrichment for DVU2413
Function | System |
---|---|
catalytic activity | go/ molecular_function |
iron-sulfur cluster binding | go/ molecular_function |
SAM_YgiQ | tigr/ tigrfam |
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Module neighborhood information for DVU2413
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0029 | hydantoinase/oxoprolinase family protein | 162, 185 | |
DVU0045 | flagellar biosynthesis protein, FliO | 185, 286 | |
DVU0048 | chemotaxis protein MotB | 185, 267 | |
DVU0055 | ispH | hydroxymethylbutenyl pyrophosphate reductase | 185, 304 |
DVU0059 | AcrB/AcrD/AcrF family protein | 185, 316 | |
DVU0110 | sigma-54 dependent transcriptional regulator/response regulator | 117, 141 | |
DVU0130 | phosphoglycolate phosphatase | 185, 247 | |
DVU0134 | glycosyl transferase group 2 family protein | 144, 185 | |
DVU0156 | ATP-dependent DNA helicase UvrD | 117, 141 | |
DVU0292 | hypothetical protein DVU0292 | 162, 185 | |
DVU0352 | aminotransferase | 141, 277 | |
DVU0392 | aromatic aminotransferase | 37, 185 | |
DVU0400 | hypothetical protein DVU0400 | 185, 292 | |
DVU0633 | penicillin-binding protein | 141, 176 | |
DVU0661 | dihydrouridine synthase family protein | 87, 185 | |
DVU0682 | DNA-binding protein | 141, 229 | |
DVU0688 | hypothetical protein DVU0688 | 185, 277 | |
DVU0723 | purT | phosphoribosylglycinamide formyltransferase 2 | 185, 278 |
DVU0818 | hypothetical protein DVU0818 | 185, 267 | |
DVU0983 | hypothetical protein DVU0983 | 35, 141 | |
DVU1113 | hypothetical protein DVU1113 | 69, 185 | |
DVU1160 | urea transporter | 161, 185 | |
DVU1181 | response regulator | 141, 279 | |
DVU1370 | hypothetical protein DVU1370 | 9, 141 | |
DVU1507 | hypothetical protein DVU1507 | 185, 225 | |
DVU1544 | mechanosensitive ion channel family protein | 117, 141 | |
DVU1581 | hypothetical protein DVU1581 | 141, 294 | |
DVU2080 | None | 185, 316 | |
DVU2233 | hypothetical protein DVU2233 | 35, 185 | |
DVU2234 | hypothetical protein DVU2234 | 69, 185 | |
DVU2302 | glutathione-regulated potassium-efflux system protein KefB | 141, 277 | |
DVU2330 | MRP family protein | 35, 141 | |
DVU2338 | HhH-GPD family DNA repair protein | 117, 141 | |
DVU2413 | radical SAM domain-containing protein | 141, 185 | |
DVU2425 | rarD | rarD protein | 141, 195 |
DVU2463 | recN | DNA repair protein RecN | 23, 141 |
DVU2493 | iron-sulfur cluster-binding protein | 185, 223 | |
DVU2520 | hypothetical protein DVU2520 | 69, 185 | |
DVU2581 | response regulator | 141, 278 | |
DVU2759 | hypothetical protein DVU2759 | 83, 185 | |
DVU2780 | hypothetical protein DVU2780 | 69, 141 | |
DVU2821 | hypothetical protein DVU2821 | 185, 316 | |
DVU2899 | hypothetical protein DVU2899 | 141, 316 | |
DVU2900 | amidohydrolase family protein | 83, 141 | |
DVU2901 | pyrB | aspartate carbamoyltransferase catalytic subunit | 141, 344 |
DVU2902 | pyrC | dihydroorotase | 141, 278 |
DVU2932 | hypothetical protein DVU2932 | 117, 141 | |
DVU3074 | hypothetical protein DVU3074 | 185, 316 | |
DVU3086 | cobB-2 | cobyrinic acid a,c-diamide synthase | 83, 141 |
DVU3087 | cobH | precorrin-8X methylmutase | 46, 141 |
DVU3091 | hypothetical protein DVU3091 | 185, 316 | |
DVU3097 | outer membrane efflux protein | 141, 249 | |
DVU3216 | sensor histidine kinase | 117, 141 | |
DVU3278 | peptidase/PDZ domain-containing protein | 83, 141 | |
DVU3321 | hypothetical protein DVU3321 | 185, 222 | |
DVU3369 | hypothetical protein DVU3369 | 185, 315 | |
DVUA0138 | sensor histidine kinase | 145, 185 |
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
Social Tab
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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.