Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0862
bifunctional flagellar protein FliS/hypothetical protein
Functional Annotations (5)
Function | System |
---|---|
Flagellin-specific chaperone FliS | cog/ cog |
bacterial-type flagellum | go/ cellular_component |
flagellum assembly | go/ biological_process |
Flagellar assembly | kegg/ kegg pathway |
fliS | tigr/ tigrfam |
Regulation information for DVU0862
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0804 | 22 | tf |
DVU1584 DVU1517 |
22 | combiner |
DVU2557 DVU2675 |
22 | combiner |
DVU2675 DVU3313 |
22 | combiner |
DVU2799 | 22 | tf |
DVU2802 DVU0569 |
22 | combiner |
DVU2802 DVU2989 |
22 | combiner |
DVU2909 DVU0110 |
22 | combiner |
DVU2909 DVU3193 |
22 | combiner |
DVU3255 DVU1561 |
22 | combiner |
DVU3313 | 22 | tf |
DVU0309 DVU3220 |
184 | combiner |
DVU1584 DVU0269 |
184 | combiner |
DVU2114 | 184 | tf |
DVU2547 DVU0309 |
184 | combiner |
DVU2547 DVU2989 |
184 | combiner |
DVU2802 DVU0110 |
184 | combiner |
DVU3255 DVU3186 |
184 | 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 |
---|---|---|---|---|
43 | 1.40e-04 | Gcatgct.ctTGCat | RegPredict | |
44 | 8.70e+00 | aAggGcGgGGaTGaCG.CTCTCc | RegPredict | |
351 | 2.20e+00 | catGGaacgttcaTTGCtt | RegPredict | |
352 | 4.10e+03 | AACACaaTGGAATAaAA | RegPredict |
Functional Enrichment for DVU0862
Function | System |
---|---|
Flagellin-specific chaperone FliS | cog/ cog |
bacterial-type flagellum | go/ cellular_component |
flagellum assembly | go/ biological_process |
Flagellar assembly | kegg/ kegg pathway |
fliS | tigr/ tigrfam |
Module neighborhood information for DVU0862
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0043 | fliQ | flagellar biosynthetic protein FliQ | 22, 286 |
DVU0044 | fliP | flagellar biosynthesis protein FliP | 184, 286 |
DVU0046 | fliN | flagellar motor switch protein FliN | 115, 184 |
DVU0047 | flagellar protein FliL | 184, 298 | |
DVU0307 | flagella basal body rod domain-containing protein | 22, 286 | |
DVU0309 | LysR family transcriptional regulator | 22, 280 | |
DVU0310 | fliI | flagellum-specific ATP synthase FliI | 125, 184 |
DVU0311 | flagellar assembly protein FliH | 125, 184 | |
DVU0312 | fliG | flagellar motor switch protein FliG | 125, 184 |
DVU0313 | fliF | flagellar M-ring protein FliF | 125, 184 |
DVU0314 | fliE | flagellar basal body component FliE | 125, 184 |
DVU0315 | flgC | flagellar basal-body rod protein FlgC | 125, 184 |
DVU0318 | hypothetical protein | 22, 286 | |
DVU0320 | hypothetical protein DVU0320 | 22, 286 | |
DVU0325 | hypD | hydrogenase expression/formation protein HypD | 22, 62 |
DVU0409 | hypothetical protein DVU0409 | 22, 184 | |
DVU0410 | hypothetical protein DVU0410 | 22, 286 | |
DVU0512 | flagellar basal-body rod protein | 125, 184 | |
DVU0513 | flgG | flagellar basal body rod protein FlgG | 125, 184 |
DVU0515 | flgH | flagellar basal body L-ring protein | 125, 184 |
DVU0516 | flgI | flagellar basal body P-ring protein | 125, 184 |
DVU0517 | M24/M37 family peptidase | 125, 184 | |
DVU0518 | hypothetical protein DVU0518 | 22, 286 | |
DVU0519 | flagellar hook-associated protein FlgK | 125, 184 | |
DVU0520 | flagellar hook-associated protein FlgL | 22, 184 | |
DVU0521 | csrA | carbon storage regulator | 184, 249 |
DVU0522 | flagellar assembly protein FliW | 184, 208 | |
DVU0858 | lipoprotein | 82, 184 | |
DVU0862 | bifunctional flagellar protein FliS/hypothetical protein | 22, 184 | |
DVU0863 | flagellar hook-associated protein 2 | 22, 184 | |
DVU0913 | hypothetical protein DVU0913 | 125, 184 | |
DVU1441 | flagellin | 22, 286 | |
DVU1443 | flgE | flagellar hook protein FlgE | 22, 286 |
DVU1444 | flgD | basal-body rod modification protein FlgD | 22, 286 |
DVU1805 | GGDEF domain-containing protein | 22, 286 | |
DVU1963 | hypothetical protein DVU1963 | 22, 286 | |
DVU2065 | hypothetical protein DVU2065 | 22, 286 | |
DVU2211 | hypothetical protein DVU2211 | 103, 184 | |
DVU2232 | hypothetical protein DVU2232 | 125, 184 | |
DVU2991 | hypothetical protein DVU2991 | 22, 286 | |
DVU3001 | hypothetical protein DVU3001 | 22, 184 | |
DVU3002 | hypothetical protein DVU3002 | 22, 286 | |
DVU3003 | radical SAM domain-containing protein | 125, 184 | |
DVU3004 | radical SAM domain-containing protein | 22, 125 | |
DVU3005 | aminotransferase | 22, 145 | |
DVU3006 | polysaccharide biosynthesis protein/methyltransferase | 22, 180 | |
DVU3014 | asparagine synthetase, glutamine-hydrolyzing | 22, 211 | |
DVU3018 | radical SAM domain-containing protein | 125, 184 | |
DVU3019 | radical SAM/B12 binding domain-containing protein | 125, 184 | |
DVU3020 | hypothetical protein DVU3020 | 125, 184 | |
DVU3232 | flhA | flagellar biosynthesis protein FlhA | 22, 286 |
Gene Page Help
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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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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.
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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.
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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.
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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)
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