Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2204 tnaA
tryptophanase
Functional Annotations (6)
Function | System |
---|---|
Tryptophanase | cog/ cog |
tryptophanase activity | go/ molecular_function |
aromatic amino acid family metabolic process | go/ biological_process |
pyridoxal phosphate binding | go/ molecular_function |
Tryptophan metabolism | kegg/ kegg pathway |
Nitrogen metabolism | kegg/ kegg pathway |
Regulation information for DVU2204
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0653 | 284 | tf |
DVU0653 DVU1744 |
284 | combiner |
DVU1517 | 284 | tf |
DVU2633 DVU1744 |
284 | combiner |
DVU2690 | 284 | tf |
DVU2886 DVU1754 |
284 | combiner |
DVUA0024 | 284 | tf |
DVUA0057 | 284 | tf |
DVUA0143 | 284 | tf |
DVU0030 DVU0525 |
133 | combiner |
DVU0230 | 133 | tf |
DVU0230 DVU1083 |
133 | combiner |
DVU0525 | 133 | tf |
DVU0653 DVU2251 |
133 | combiner |
DVU1754 DVU0030 |
133 | combiner |
DVU1754 DVU2785 |
133 | combiner |
DVU1967 | 133 | tf |
DVU2036 DVU2251 |
133 | 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 |
---|---|---|---|---|
257 | 1.00e-06 | aGgagaAggGa.ggcagttcaaGC | RegPredict | |
258 | 3.70e-04 | aAaGGaaAAGaCAAccGCCTtcCA | RegPredict | |
543 | 7.00e+01 | gC.CacCATCc | RegPredict | |
544 | 5.00e+02 | gCCttCGgCAacGtc | RegPredict |
Functional Enrichment for DVU2204
Function | System |
---|---|
Tryptophanase | cog/ cog |
tryptophanase activity | go/ molecular_function |
aromatic amino acid family metabolic process | go/ biological_process |
pyridoxal phosphate binding | go/ molecular_function |
Tryptophan metabolism | kegg/ kegg pathway |
Nitrogen metabolism | kegg/ kegg pathway |
Module neighborhood information for DVU2204
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0008 | hypothetical protein DVU0008 | 39, 284 | |
DVU0181 | modB | molybdenum ABC transporter permease | 284, 329 |
DVU0185 | hypothetical protein DVU0185 | 284, 299 | |
DVU0283 | AhpF family protein/thioredoxin reductase | 284, 329 | |
DVU0529 | Rrf2 family transcriptional regulator | 133, 189 | |
DVU0530 | response regulator, rrf1 protein | 133, 189 | |
DVU0531 | hmc operon protein 6 | 133, 189 | |
DVU0532 | hmc operon protein 5 | 133, 189 | |
DVU0535 | hmc operon protein 2 | 133, 189 | |
DVU0536 | hmcA | high-molecular-weight cytochrome C | 133, 189 |
DVU0877 | hypothetical protein DVU0877 | 160, 284 | |
DVU0878 | dnaK suppressor protein | 133, 202 | |
DVU0926 | hypothetical protein DVU0926 | 133, 244 | |
DVU0929 | obgE | GTPase ObgE | 133, 244 |
DVU0930 | proB | gamma-glutamyl kinase | 30, 133 |
DVU1416 | hypothetical protein DVU1416 | 284, 329 | |
DVU1505 | holin | 133, 152 | |
DVU1506 | hypothetical protein DVU1506 | 133, 152 | |
DVU1755 | hypothetical protein DVU1755 | 118, 133 | |
DVU1899 | DNA repair protein RecO | 25, 284 | |
DVU2147 | L-serine dehydratase | 68, 284 | |
DVU2204 | tnaA | tryptophanase | 133, 284 |
DVU2303 | hypothetical protein DVU2303 | 51, 284 | |
DVU2334 | hypothetical protein DVU2334 | 284, 329 | |
DVU2346 | hypothetical protein DVU2346 | 284, 329 | |
DVU2814 | hypothetical protein DVU2814 | 133, 256 | |
DVU2815 | outer membrane efflux protein | 133, 256 | |
DVU2816 | multidrug resistance protein | 133, 256 | |
DVU2817 | multidrug resistance protein | 133, 256 | |
DVU2818 | hypothetical protein DVU2818 | 133, 256 | |
DVU2819 | TetR family transcriptional regulator | 133, 256 | |
DVU3000 | hypothetical protein DVU3000 | 15, 284 | |
DVU3007 | hypothetical protein DVU3007 | 15, 284 | |
DVU3034 | hypothetical protein DVU3034 | 36, 284 | |
DVU3057 | oxygen-independent coproporphyrinogen III oxidase | 82, 284 | |
DVU3214 | phosphoenolpyruvate synthase-like protein | 67, 284 | |
DVU3280 | None | 7, 133 |
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;- 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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