Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2461
oligopeptide ABC transporter permease
Functional Annotations (6)
Function | System |
---|---|
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components | cog/ cog |
alkaline phosphatase activity | go/ molecular_function |
transporter activity | go/ molecular_function |
transport | go/ biological_process |
membrane | go/ cellular_component |
ABC transporters | kegg/ kegg pathway |
Regulation information for DVU2461
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0653 | 9 | tf |
DVU1561 | 9 | tf |
DVU1561 DVU0230 |
9 | combiner |
DVU2275 | 9 | tf |
DVU3023 | 9 | tf |
DVU3167 DVU0569 |
9 | combiner |
DVU3167 DVU1730 |
9 | combiner |
DVUA0024 | 9 | tf |
DVU1063 | 69 | tf |
DVU1063 DVU2934 |
69 | combiner |
DVU1744 | 69 | tf |
DVU2633 DVU1730 |
69 | combiner |
DVU2788 DVU1744 |
69 | combiner |
DVU3066 DVU2690 |
69 | combiner |
DVU3111 DVU1402 |
69 | combiner |
DVU3142 DVU0529 |
69 | combiner |
DVUA0100 DVU1063 |
69 | 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 |
---|---|---|---|---|
17 | 1.20e+04 | agcgGgCaTgG | RegPredict | |
18 | 1.30e+04 | TcCTGaaAacC | RegPredict | |
135 | 1.60e+02 | ttCattcTcttttccgGtcgCgca | RegPredict | |
136 | 4.40e+03 | ATGACa | RegPredict |
Functional Enrichment for DVU2461
Function | System |
---|---|
ABC-type dipeptide/oligopeptide/nickel transport systems, permease components | cog/ cog |
alkaline phosphatase activity | go/ molecular_function |
transporter activity | go/ molecular_function |
transport | go/ biological_process |
membrane | go/ cellular_component |
ABC transporters | kegg/ kegg pathway |
Module neighborhood information for DVU2461
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0038 | acyltransferase domain-containing protein | 69, 161 | |
DVU0084 | aIF-2BI family translation initiation factor | 9, 23 | |
DVU0087 | hypothetical protein DVU0087 | 9, 44 | |
DVU0088 | panF | sodium/panthothenate symporter | 9, 69 |
DVU0091 | hypothetical protein DVU0091 | 9, 327 | |
DVU0101 | UbiE/COQ5 family methlytransferase | 69, 247 | |
DVU0104 | cation ABC transporter permease | 69, 162 | |
DVU0141 | M50 family peptidase | 9, 223 | |
DVU0142 | trpS | tryptophanyl-tRNA synthetase | 9, 180 |
DVU0236 | phage integrase family site specific recombinase | 54, 69 | |
DVU0249 | hypothetical protein DVU0249 | 69, 181 | |
DVU0257 | acetyltransferase | 37, 69 | |
DVU0323 | folD | bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase | 9, 223 |
DVU0324 | hypothetical protein DVU0324 | 9, 181 | |
DVU0345 | hypothetical protein DVU0345 | 46, 69 | |
DVU0651 | hypothetical protein DVU0651 | 9, 334 | |
DVU0794 | fabI | enoyl-ACP reductase | 9, 113 |
DVU0859 | hypothetical protein DVU0859 | 69, 162 | |
DVU1029 | hisC | histidinol-phosphate aminotransferase | 9, 223 |
DVU1036 | hypothetical protein DVU1036 | 69, 334 | |
DVU1113 | hypothetical protein DVU1113 | 69, 185 | |
DVU1165 | pyridine nucleotide-disulfide oxidoreductase | 69, 330 | |
DVU1185 | colicin V production family protein | 9, 180 | |
DVU1189 | hypothetical protein DVU1189 | 9, 277 | |
DVU1213 | rhomboid family protein | 69, 120 | |
DVU1269 | hypothetical protein DVU1269 | 69, 172 | |
DVU1369 | hypothetical protein DVU1369 | 9, 126 | |
DVU1370 | hypothetical protein DVU1370 | 9, 141 | |
DVU1389 | hypothetical protein DVU1389 | 69, 162 | |
DVU1391 | hypothetical protein DVU1391 | 69, 87 | |
DVU1435 | hypothetical protein DVU1435 | 69, 87 | |
DVU1459 | hypothetical protein DVU1459 | 9, 334 | |
DVU1540 | purU | formyltetrahydrofolate deformylase | 9, 223 |
DVU1860 | lnt | apolipoprotein N-acyltransferase | 9, 214 |
DVU1863 | flagellar synthesis regulator FleN | 9, 113 | |
DVU1958 | sensory box histidine kinase | 69, 192 | |
DVU2234 | hypothetical protein DVU2234 | 69, 185 | |
DVU2257 | hypothetical protein DVU2257 | 9, 214 | |
DVU2276 | hypothetical protein DVU2276 | 69, 334 | |
DVU2320 | 3-octaprenyl-4-hydroxybenzoate carboxy-lyase | 9, 316 | |
DVU2366 | hypothetical protein DVU2366 | 69, 155 | |
DVU2408 | hypothetical protein DVU2408 | 69, 269 | |
DVU2461 | oligopeptide ABC transporter permease | 9, 69 | |
DVU2465 | hypothetical protein DVU2465 | 69, 245 | |
DVU2520 | hypothetical protein DVU2520 | 69, 185 | |
DVU2558 | bioB | biotin synthase | 9, 327 |
DVU2570 | GGDEF domain/HAMP domain-containing protein | 69, 247 | |
DVU2594 | hypothetical protein DVU2594 | 69, 275 | |
DVU2634 | hypothetical protein DVU2634 | 5, 9 | |
DVU2660 | hypothetical protein DVU2660 | 69, 275 | |
DVU2700 | hypothetical protein DVU2700 | 33, 69 | |
DVU2780 | hypothetical protein DVU2780 | 69, 141 | |
DVU2823 | TRAP transporter subunit DctMQ | 69, 181 | |
DVU2908 | hypothetical protein DVU2908 | 69, 334 | |
DVU2910 | hypothetical protein DVU2910 | 69, 113 | |
DVU2953 | GntR family transcriptional regulator | 35, 69 | |
DVU2954 | GGDEF domain-containing protein | 69, 334 | |
DVU2955 | hypothetical protein DVU2955 | 69, 334 | |
DVU3017 | hypothetical protein DVU3017 | 69, 87 | |
DVU3040 | hypothetical protein DVU3040 | 69, 181 | |
DVU3297 | tryptophan-specific transport protein | 9, 334 | |
DVU3386 | permease | 69, 222 |
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
- 5. Module(s) that source gene and target genes belong to
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