Organism : Desulfovibrio vulgaris Hildenborough
| Module List :
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DVU3319 putA
proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase
Functional Annotations (11)
Function | System |
---|---|
Delta 1-pyrroline-5-carboxylate dehydrogenase | cog/ cog |
1-pyrroline-5-carboxylate dehydrogenase activity | go/ molecular_function |
proline dehydrogenase activity | go/ molecular_function |
glutamate biosynthetic process | go/ biological_process |
proline biosynthetic process | go/ biological_process |
proline catabolic process | go/ biological_process |
Alanine aspartate and glutamate metabolism | kegg/ kegg pathway |
Arginine and proline metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
D1pyr5carbox2 | tigr/ tigrfam |
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Regulation information for DVU3319
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0277 DVU2547 |
153 | combiner |
DVU0309 DVU1788 |
153 | combiner |
DVU0629 | 153 | tf |
DVU2547 DVU2114 |
153 | combiner |
DVU2557 DVU2547 |
153 | combiner |
DVU2557 DVU2675 |
153 | combiner |
DVU2909 DVU1949 |
153 | combiner |
DVUA0151 DVU1788 |
153 | combiner |
DVU0230 DVU1949 |
348 | combiner |
DVU0277 DVU0118 |
348 | combiner |
DVU0277 DVU2894 |
348 | combiner |
DVU0653 DVU2251 |
348 | combiner |
DVU0946 DVU2251 |
348 | combiner |
DVU1788 | 348 | tf |
DVU2547 DVU0110 |
348 | combiner |
DVU2547 DVU2251 |
348 | combiner |
DVU2547 DVU3193 |
348 | combiner |
DVU2909 | 348 | tf |
DVU3220 DVU2251 |
348 | 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 |
---|---|---|---|---|
291 | 2.30e-03 | cAGCAaGGAG |
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RegPredict |
292 | 4.70e+00 | GGCA.GAtGCc |
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RegPredict |
661 | 6.00e+02 | CtTTccaGCcgtcCcGACgtCgGa |
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RegPredict |
662 | 1.60e+03 | ctgaC.tcCaTaacggtctggtac |
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RegPredict |
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Functional Enrichment for DVU3319
Function | System |
---|---|
Delta 1-pyrroline-5-carboxylate dehydrogenase | cog/ cog |
1-pyrroline-5-carboxylate dehydrogenase activity | go/ molecular_function |
proline dehydrogenase activity | go/ molecular_function |
glutamate biosynthetic process | go/ biological_process |
proline biosynthetic process | go/ biological_process |
proline catabolic process | go/ biological_process |
Alanine aspartate and glutamate metabolism | kegg/ kegg pathway |
Arginine and proline metabolism | kegg/ kegg pathway |
Metabolic pathways | kegg/ kegg pathway |
Biosynthesis of secondary metabolites | kegg/ kegg pathway |
D1pyr5carbox2 | tigr/ tigrfam |
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Module neighborhood information for DVU3319
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0019 | ngr | nigerythrin | 60, 348 |
DVU0068 | hypothetical protein DVU0068 | 107, 153 | |
DVU0092 | sensory box histidine kinase | 145, 348 | |
DVU0175 | tungsten formylmethanofuran dehydrogenase family protein/molybdopterin binding protein | 192, 348 | |
DVU0239 | hypothetical protein DVU0239 | 153, 274 | |
DVU0253 | oxidoreductase | 148, 153 | |
DVU0260 | response regulator | 346, 348 | |
DVU0263 | acidic cytochrome c3 | 346, 348 | |
DVU0264 | ferredoxin, 4Fe-4S | 346, 348 | |
DVU0402 | dsvA | dissimilatory sulfite reductase subunit alpha | 292, 348 |
DVU0403 | dvsB | dissimilatory sulfite reductase subunit beta | 292, 348 |
DVU0404 | dissimilatory sulfite reductase B | 292, 348 | |
DVU0411 | heptosyltransferase family protein | 153, 342 | |
DVU0456 | DHH family protein | 153, 192 | |
DVU0624 | NapC/NirT cytochrome c family protein | 153, 255 | |
DVU0625 | cytochrome c nitrite reductase, catalytic subunit NfrA | 153, 255 | |
DVU0676 | His/Glu/Gln/Arg/opine ABC transporter permease | 153, 198 | |
DVU0701 | glcB | malate synthase G | 192, 348 |
DVU0819 | FMN reductase, NADPH-dependent | 153, 274 | |
DVU0979 | dihydroxyacetone kinase subunit DhaK | 60, 348 | |
DVU0980 | DAK2 domain-containing protein | 6, 348 | |
DVU0995 | ThiJ/PfpI family protein | 60, 153 | |
DVU1179 | aor | tungsten-containing aldehyde:ferredoxin oxidoreductase | 157, 348 |
DVU1569 | porA | pyruvate ferredoxin oxidoreductase subunit alpha | 148, 153 |
DVU1570 | porB | pyruvate ferredoxin oxidoreductase subunit beta | 77, 153 |
DVU1681 | mreB-2 | rod shape-determining protein MreB | 318, 348 |
DVU1684 | gcvT | glycine cleavage system T protein | 318, 348 |
DVU1685 | 16S ribosomal RNA methyltransferase RsmE | 318, 348 | |
DVU1686 | recombination factor protein RarA | 318, 348 | |
DVU1816 | hypothetical protein DVU1816 | 148, 153 | |
DVU1917 | hysB | periplasmic | 139, 348 |
DVU1918 | hysA | periplasmic | 139, 348 |
DVU1921 | hynB-1 | periplasmic | 229, 348 |
DVU1922 | hynA-1 | periplasmic | 229, 348 |
DVU2109 | hypothetical protein DVU2109 | 236, 348 | |
DVU2348 | dut | deoxyuridine 5'-triphosphate nucleotidohydrolase | 153, 262 |
DVU2481 | formate dehydrogenase subunit beta | 77, 348 | |
DVU2482 | fdnG-2 | formate dehydrogenase subunit alpha, selenocysteine-containing | 192, 348 |
DVU2483 | cytochrome c family protein | 77, 348 | |
DVU2514 | pyk | pyruvate kinase | 249, 348 |
DVU2543 | hydroxylamine reductase | 153, 304 | |
DVU2544 | iron-sulfur cluster-binding protein | 153, 161 | |
DVU2557 | birA | birA bifunctional protein | 148, 348 |
DVU2589 | hypothetical protein DVU2589 | 37, 153 | |
DVU2590 | sensory box protein | 37, 153 | |
DVU3037 | rhodanese-like domain-containing protein | 192, 348 | |
DVU3183 | rbO | desulfoferrodoxin | 60, 348 |
DVU3184 | rubredoxin | 60, 348 | |
DVU3185 | roO | rubredoxin-oxygen oxidoreductase | 60, 348 |
DVU3259 | xth | exodeoxyribonuclease III | 153, 296 |
DVU3262 | fdrA | fumarate reductase flavoprotein subunit | 153, 348 |
DVU3263 | frdB | fumarate reductase iron-sulfur subunit | 148, 348 |
DVU3293 | acetolactate synthase | 60, 348 | |
DVU3294 | aldehyde dehydrogenase family protein | 153, 348 | |
DVU3319 | putA | proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase | 153, 348 |
DVUA0095 | hypothetical protein DVUA0095 | 153, 315 |
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.