Organism : Desulfovibrio vulgaris Hildenborough
| Module List :
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DVU3010
aminotransferase
Functional Annotations (3)
Function | System |
---|---|
Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis | cog/ cog |
catalytic activity | go/ molecular_function |
pyridoxal phosphate binding | go/ molecular_function |
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Regulation information for DVU3010
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0539 DVU1745 |
112 | combiner |
DVU1645 DVU2275 |
112 | combiner |
DVU1645 DVU3255 |
112 | combiner |
DVU2195 | 112 | tf |
DVU2547 DVU0539 |
112 | combiner |
DVU2547 DVU3142 |
112 | combiner |
DVU3080 DVU2275 |
112 | combiner |
DVU1645 DVU3193 |
304 | combiner |
DVU1674 DVU3095 |
304 | combiner |
DVU1674 DVU3186 |
304 | combiner |
DVU2319 | 304 | tf |
DVU2547 DVU2934 |
304 | combiner |
DVU2644 | 304 | tf |
DVU2644 DVU2799 |
304 | combiner |
DVU2934 DVU0621 |
304 | combiner |
DVU3084 | 304 | tf |
DVU3193 DVU2114 |
304 | 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 |
---|---|---|---|---|
215 | 3.00e+04 | ACTTCaCgaC |
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RegPredict |
216 | 6.50e+03 | GCCcGaAcgGttGacGcGTTCGcC |
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RegPredict |
581 | 5.20e+04 | TcCATGTCacA |
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RegPredict |
582 | 2.00e+04 | CggaTGCCCTG |
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RegPredict |
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Functional Enrichment for DVU3010
Function | System |
---|---|
Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis | cog/ cog |
catalytic activity | go/ molecular_function |
pyridoxal phosphate binding | go/ molecular_function |
![](/static/images/help.png)
Module neighborhood information for DVU3010
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0032 | hypothetical protein DVU0032 | 112, 211 | |
DVU0055 | ispH | hydroxymethylbutenyl pyrophosphate reductase | 185, 304 |
DVU0118 | sigma-54 dependent transcriptional regulator/response regulator | 105, 112 | |
DVU0119 | sensor histidine kinase | 82, 112 | |
DVU0120 | ABC transporter substrate-binding protein | 82, 112 | |
DVU0187 | GGDEF domain-containing protein | 258, 304 | |
DVU0245 | protein phosphatase | 46, 304 | |
DVU0289 | moaC | molybdenum cofactor biosynthesis protein C | 105, 112 |
DVU0412 | potassium uptake protein TrkA | 46, 304 | |
DVU0482 | sensory box histidine kinase/response regulator | 105, 112 | |
DVU0581 | response regulator/anti-anti-sigma factor | 105, 112 | |
DVU0582 | sensory box histidine kinase | 105, 112 | |
DVU0584 | transposase | 105, 304 | |
DVU0631 | hypothetical protein DVU0631 | 109, 112 | |
DVU0634 | hypothetical protein DVU0634 | 105, 112 | |
DVU0687 | tungsten-containing aldehyde:ferredoxin oxidoreductase | 82, 304 | |
DVU0689 | rnhA | ribonuclease H | 82, 304 |
DVU0749 | DNA-binding response regulator | 26, 304 | |
DVU0814 | bacterioferritin comigratory protein | 112, 211 | |
DVU0897 | RNA modification protein | 172, 304 | |
DVU0898 | hypothetical protein DVU0898 | 172, 304 | |
DVU0900 | gmk | guanylate kinase | 172, 304 |
DVU0901 | pyrF | orotidine 5`-phosphate decarboxylase | 32, 304 |
DVU0922 | cytochrome c family protein | 304, 307 | |
DVU0996 | hypothetical protein DVU0996 | 304, 307 | |
DVU1136 | host-nuclease inhibitor protein Gam | 112, 231 | |
DVU1188 | hypothetical protein DVU1188 | 211, 304 | |
DVU1219 | hypothetical protein DVU1219 | 35, 112 | |
DVU1338 | hypothetical protein DVU1338 | 112, 198 | |
DVU1419 | sigma-54 dependent transcriptional regulator/response regulator | 112, 123 | |
DVU1536 | Slt family transglycosylase | 12, 304 | |
DVU1547 | sensory box protein | 35, 112 | |
DVU1549 | hypothetical protein DVU1549 | 112, 198 | |
DVU2092 | thiamine biosynthesis protein ThiF | 161, 304 | |
DVU2337 | M24/M37 family peptidase | 26, 112 | |
DVU2352 | glycosyl transferase group 2 family protein | 76, 112 | |
DVU2365 | hypothetical protein DVU2365 | 304, 315 | |
DVU2472 | hypothetical protein DVU2472 | 105, 112 | |
DVU2477 | pstS | phosphate ABC transporter periplasmic phosphate-binding protein PstS | 211, 304 |
DVU2479 | phosphate ABC transporter permease | 211, 304 | |
DVU2543 | hydroxylamine reductase | 153, 304 | |
DVU2588 | DNA-binding response regulator | 112, 281 | |
DVU2732 | hypothetical protein DVU2732 | 38, 112 | |
DVU2739 | pyruvate phosphate dikinase PEP/pyruvate binding subunit | 112, 304 | |
DVU2749 | cobL | precorrin-6Y C5,15-methyltransferase (decarboxylating) | 166, 304 |
DVU2886 | AraC family transcriptional regulator | 251, 304 | |
DVU2896 | hypothetical protein | 30, 112 | |
DVU2947 | anaerobic ribonucleoside triphosphate reductase | 81, 304 | |
DVU2961 | hypothetical protein DVU2961 | 285, 304 | |
DVU2994 | glycosyl transferase group 2 family protein | 15, 112 | |
DVU3010 | aminotransferase | 112, 304 | |
DVU3012 | hypothetical protein DVU3012 | 95, 112 | |
DVU3153 | hypothetical protein DVU3153 | 112, 115 | |
DVU3209 | hypothetical protein DVU3209 | 112, 211 | |
DVU3229 | fliA | RNA polymerase sigma factor for flagellar operon FliA | 251, 304 |
DVU3336 | potassium channel histidine kinase domain-containing protein/universal stress protein | 13, 112 | |
DVU3388 | lipoprotein | 105, 112 | |
DVUA0072 | glycosyl transferase, group 1 family protein | 255, 304 |
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.
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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;![](/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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