Organism : Desulfovibrio vulgaris Hildenborough
| Module List :
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DVU0175
tungsten formylmethanofuran dehydrogenase family protein/molybdopterin binding protein
Functional Annotations (2)
Function | System |
---|---|
Molybdopterin biosynthesis enzyme | cog/ cog |
Mo-molybdopterin cofactor biosynthetic process | go/ biological_process |
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Regulation information for DVU0175
(Mouseover regulator name to see its description)
Regulator | Module | Operator |
---|---|---|
DVU0110 DVU1419 |
192 | combiner |
DVU1572 DVU2547 |
192 | combiner |
DVU2275 | 192 | tf |
DVU2527 DVU1949 |
192 | combiner |
DVU2547 | 192 | tf |
DVU2547 DVU0110 |
192 | combiner |
DVU2547 DVU2675 |
192 | combiner |
DVU2547 DVU2799 |
192 | combiner |
DVU2557 | 192 | tf |
DVU2557 DVU2675 |
192 | combiner |
DVU2675 | 192 | tf |
DVU2909 | 192 | tf |
DVU3066 | 192 | tf |
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 |
---|---|---|---|---|
367 | 1.00e-02 | gGcttTGGCGT |
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RegPredict |
368 | 4.20e+02 | GCAtCGcAtgt |
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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 DVU0175
Function | System |
---|---|
Molybdopterin biosynthesis enzyme | cog/ cog |
Mo-molybdopterin cofactor biosynthetic process | go/ biological_process |
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Module neighborhood information for DVU0175
Gene | Common Name | Description | Module membership |
---|---|---|---|
DVU0019 | ngr | nigerythrin | 60, 348 |
DVU0092 | sensory box histidine kinase | 145, 348 | |
DVU0175 | tungsten formylmethanofuran dehydrogenase family protein/molybdopterin binding protein | 192, 348 | |
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 | |
DVU0456 | DHH family protein | 153, 192 | |
DVU0580 | moaA | molybdenum cofactor biosynthesis protein A | 192, 281 |
DVU0600 | ldh | L-lactate dehydrogenase | 192, 281 |
DVU0626 | ilvN-1 | acetolactate synthase small subunit | 192, 298 |
DVU0627 | ptB | phosphotransbutyrylase | 192, 229 |
DVU0701 | glcB | malate synthase G | 192, 348 |
DVU0979 | dihydroxyacetone kinase subunit DhaK | 60, 348 | |
DVU0980 | DAK2 domain-containing protein | 6, 348 | |
DVU1037 | mercuric reductase | 181, 192 | |
DVU1179 | aor | tungsten-containing aldehyde:ferredoxin oxidoreductase | 157, 348 |
DVU1396 | hypothetical protein DVU1396 | 192, 274 | |
DVU1413 | hypothetical protein DVU1413 | 192, 296 | |
DVU1420 | Hpt domain-containing protein | 109, 192 | |
DVU1471 | HSP20 family protein | 71, 192 | |
DVU1472 | ATP-dependent protease | 115, 192 | |
DVU1592 | arginine N-succinyltransferase subunit beta | 192, 274 | |
DVU1594 | cheA-1 | chemotaxis protein CheA | 192, 274 |
DVU1596 | cheB-1 | protein-glutamate methylesterase CheB | 192, 274 |
DVU1613 | glutamate synthase subunit beta | 192, 236 | |
DVU1614 | iron-sulfur cluster-binding protein | 6, 192 | |
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 | |
DVU1917 | hysB | periplasmic | 139, 348 |
DVU1918 | hysA | periplasmic | 139, 348 |
DVU1921 | hynB-1 | periplasmic | 229, 348 |
DVU1922 | hynA-1 | periplasmic | 229, 348 |
DVU1958 | sensory box histidine kinase | 69, 192 | |
DVU1986 | hypothetical protein DVU1986 | 192, 198 | |
DVU2109 | hypothetical protein DVU2109 | 236, 348 | |
DVU2349 | carbohydrate phosphorylase family protein | 60, 192 | |
DVU2360 | FAD/NAD-binding family oxidoreductase | 115, 192 | |
DVU2421 | 4-oxalocrotonate tautomerase family protein | 192, 274 | |
DVU2422 | nitroreductase family protein | 192, 274 | |
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 |
DVU2557 | birA | birA bifunctional protein | 148, 348 |
DVU2895 | hypothetical protein DVU2895 | 115, 192 | |
DVU2968 | sensor histidine kinase/response regulator | 148, 192 | |
DVU2976 | hypothetical protein DVU2976 | 83, 192 | |
DVU3037 | rhodanese-like domain-containing protein | 192, 348 | |
DVU3077 | AhpC/TSA family protein | 192, 269 | |
DVU3147 | 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase | 192, 214 | |
DVU3148 | malQ | 4-alpha-glucanotransferase | 27, 192 |
DVU3183 | rbO | desulfoferrodoxin | 60, 348 |
DVU3184 | rubredoxin | 60, 348 | |
DVU3185 | roO | rubredoxin-oxygen oxidoreductase | 60, 348 |
DVU3217 | hypothetical protein DVU3217 | 109, 192 | |
DVU3262 | fdrA | fumarate reductase flavoprotein subunit | 153, 348 |
DVU3263 | frdB | fumarate reductase iron-sulfur subunit | 148, 348 |
DVU3282 | ADP-ribosylglycohydrolase family protein | 109, 192 | |
DVU3293 | acetolactate synthase | 60, 348 | |
DVU3294 | aldehyde dehydrogenase family protein | 153, 348 | |
DVU3319 | putA | proline dehydrogenase/delta-1-pyrroline-5-carboxylate dehydrogenase | 153, 348 |
DVUA0021 | hypothetical protein DVUA0021 | 61, 192 | |
DVUA0023 | ABC transporter permease | 192, 274 | |
DVUA0091 | katA | catalase | 192, 274 |
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.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.
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
Social Tab
Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.
Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.
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.