Organism : Desulfovibrio vulgaris Hildenborough
| Module List :
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DVU0587 fdnG-1
formate dehydrogenase subunit alpha, selenocysteine-containing
Functional Annotations (12)
Function | System |
---|---|
Anaerobic dehydrogenases, typically selenocysteine-containing | cog/ cog |
cytoplasm | go/ cellular_component |
electron transport | go/ biological_process |
formate dehydrogenase (NAD+) activity | go/ molecular_function |
formate dehydrogenase complex | go/ cellular_component |
molybdenum ion binding | go/ molecular_function |
cellular respiration | go/ biological_process |
Glyoxylate and dicarboxylate metabolism | kegg/ kegg pathway |
Methane metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Microbial metabolism in diverse environments | kegg/ kegg pathway |
TAT_signal_seq | tigr/ tigrfam |
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Regulation information for DVU0587
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0813 | 167 | tf |
DVU0946 DVU0269 |
167 | combiner |
DVU1584 | 167 | tf |
DVU1628 DVU0813 |
167 | combiner |
DVU1949 | 167 | tf |
DVU2086 DVU0744 |
167 | combiner |
DVU2275 DVU0269 |
167 | combiner |
DVU2547 | 167 | tf |
DVU2547 DVU0230 |
167 | combiner |
DVU3381 | 167 | tf |
DVU0309 DVU1949 |
274 | combiner |
DVU0309 DVU2275 |
274 | combiner |
DVU1402 | 274 | tf |
DVU1572 DVU2547 |
274 | combiner |
DVU2547 DVU1340 |
274 | combiner |
DVU2547 DVU2394 |
274 | combiner |
DVU2557 DVU2547 |
274 | combiner |
DVU2557 DVU2675 |
274 | combiner |
DVU2675 | 274 | tf |
DVU3066 | 274 | tf |
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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 |
---|---|---|---|---|
319 | 1.10e-04 | ATcaATTcAcaAAGaCaGGAGCCG |
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RegPredict |
320 | 4.40e-02 | CTCCACGgccatcatccGcAA |
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RegPredict |
523 | 1.70e+02 | ATg.atcgaTgtaatGgatt |
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RegPredict |
524 | 8.90e+03 | gTaCaTggcGcAaGcctcTGaacA |
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RegPredict |
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Functional Enrichment for DVU0587
Function | System |
---|---|
Anaerobic dehydrogenases, typically selenocysteine-containing | cog/ cog |
cytoplasm | go/ cellular_component |
electron transport | go/ biological_process |
formate dehydrogenase (NAD+) activity | go/ molecular_function |
formate dehydrogenase complex | go/ cellular_component |
molybdenum ion binding | go/ molecular_function |
cellular respiration | go/ biological_process |
Glyoxylate and dicarboxylate metabolism | kegg/ kegg pathway |
Methane metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Microbial metabolism in diverse environments | kegg/ kegg pathway |
TAT_signal_seq | tigr/ tigrfam |
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Module neighborhood information for DVU0587
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0111 | response regulator | 143, 274 | |
DVU0131 | hypothetical protein DVU0131 | 167, 222 | |
DVU0132 | hypothetical protein DVU0132 | 167, 222 | |
DVU0133 | hypothetical protein DVU0133 | 167, 222 | |
DVU0239 | hypothetical protein DVU0239 | 153, 274 | |
DVU0254 | hypothetical protein DVU0254 | 105, 167 | |
DVU0401 | hypothetical protein DVU0401 | 32, 167 | |
DVU0453 | ATP-dependent DNA helicase UvrD | 71, 274 | |
DVU0577 | formate dehydrogenase formation protein FdhE | 274, 281 | |
DVU0579 | molybdopterin-guanine dinucleotide biosynthesis protein A | 274, 281 | |
DVU0587 | fdnG-1 | formate dehydrogenase subunit alpha, selenocysteine-containing | 167, 274 |
DVU0684 | hflK protein | 167, 194 | |
DVU0819 | FMN reductase, NADPH-dependent | 153, 274 | |
DVU1382 | HesB family selenoprotein | 167, 226 | |
DVU1383 | hypothetical protein DVU1383 | 57, 167 | |
DVU1396 | hypothetical protein DVU1396 | 192, 274 | |
DVU1397 | bfr | bacterioferritin | 60, 274 |
DVU1412 | glycerate dehydrogenase | 236, 274 | |
DVU1564 | hypothetical protein DVU1564 | 263, 274 | |
DVU1592 | arginine N-succinyltransferase subunit beta | 192, 274 | |
DVU1593 | cheY-1 | chemotaxis protein CheY | 123, 274 |
DVU1594 | cheA-1 | chemotaxis protein CheA | 192, 274 |
DVU1595 | cheR-1 | chemotaxis protein methyltransferase | 274, 277 |
DVU1596 | cheB-1 | protein-glutamate methylesterase CheB | 192, 274 |
DVU1597 | sulfite reductase, assimilatory-type | 123, 274 | |
DVU1722 | hypothetical protein DVU1722 | 119, 167 | |
DVU1838 | trxB-2 | thioredoxin-disulfide reductase | 167, 222 |
DVU1839 | trx | thioredoxin | 4, 167 |
DVU1943 | hypothetical protein DVU1943 | 167, 226 | |
DVU1973 | rhodanese-like domain-containing protein | 269, 274 | |
DVU1974 | pyridine nucleotide-disulfide oxidoreductase | 274, 283 | |
DVU2044 | hypothetical protein DVU2044 | 167, 196 | |
DVU2421 | 4-oxalocrotonate tautomerase family protein | 192, 274 | |
DVU2422 | nitroreductase family protein | 192, 274 | |
DVU2469 | hypothetical protein DVU2469 | 4, 167 | |
DVU2486 | acetyltransferase | 119, 167 | |
DVU2489 | hypothetical protein DVU2489 | 167, 194 | |
DVU2972 | chemotaxis protein CheD | 37, 274 | |
DVU3041 | cytochrome c553 | 178, 274 | |
DVU3042 | lipoprotein | 60, 274 | |
DVU3076 | hypothetical protein DVU3076 | 269, 274 | |
DVU3079 | glyoxalase family protein | 110, 274 | |
DVU3135 | flavodoxin-like fold domain-containing protein | 110, 274 | |
DVU3136 | nitroreductase family protein | 110, 274 | |
DVU3344 | hypothetical protein DVU3344 | 167, 194 | |
DVU3346 | hypothetical protein DVU3346 | 120, 167 | |
DVUA0023 | ABC transporter permease | 192, 274 | |
DVUA0029 | hypothetical protein DVUA0029 | 167, 222 | |
DVUA0091 | katA | catalase | 192, 274 |
DVUA0127 | None | 167, 265 |
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
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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.