Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3392 glnA

glutamine synthetase, type I

CircVis
Functional Annotations (11)
Function System
Glutamine synthetase cog/ cog
glutamate-ammonia ligase activity go/ molecular_function
cytoplasm go/ cellular_component
glutamine biosynthetic process go/ biological_process
nitrogen fixation go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3392
(Mouseover regulator name to see its description)

DVU3392 is regulated by 20 influences and regulates 0 modules.
Regulators for DVU3392 glnA (20)
Regulator Module Operator
DVU0230
DVU1083
135 combiner
DVU0277
DVU0629
135 combiner
DVU0525 135 tf
DVU0629 135 tf
DVU1754
DVU1083
135 combiner
DVU2036
DVU2114
135 combiner
DVU2557
DVU3255
135 combiner
DVU3255
DVU1690
135 combiner
DVU3255
DVU2835
135 combiner
DVUA0143 135 tf
DVU0110
DVU1419
60 combiner
DVU1144 60 tf
DVU1949 60 tf
DVU2547
DVU2251
60 combiner
DVU2557
DVU1419
60 combiner
DVU2557
DVU2547
60 combiner
DVU2788
DVU2394
60 combiner
DVU2788
DVU2557
60 combiner
DVU2909
DVU1949
60 combiner
DVU3084
DVU1419
60 combiner

Warning: DVU3392 Does not regulate any modules!

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 Table (4)
Motif Id e-value Consensus Motif Logo RegPredict
117 2.80e+02 ACATAGAGAGAGGTTACAAAAGAT
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RegPredict
118 2.50e+02 aTgtacggGaAaAtcCacA
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RegPredict
261 1.90e+00 AAaatTgAaAAgacAatcgT
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RegPredict
262 5.00e+03 agtcTaGGAaaaTcGcacacG
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RegPredict
Motif Help

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for DVU3392

DVU3392 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Glutamine synthetase cog/ cog
glutamate-ammonia ligase activity go/ molecular_function
cytoplasm go/ cellular_component
glutamine biosynthetic process go/ biological_process
nitrogen fixation go/ biological_process
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Arginine and proline metabolism kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Two-component system kegg/ kegg pathway
Module neighborhood information for DVU3392

DVU3392 has total of 50 gene neighbors in modules 60, 135
Gene neighbors (50)
Gene Common Name Description Module membership
DVU0019 ngr nigerythrin 60, 348
DVU0079 ZIP zinc transporter family protein 48, 135
DVU0276 hypothetical protein DVU0276 60, 71
DVU0299 anaerobic ribonucleoside triphosphate reductase 135, 268
DVU0300 radical SAM domain-containing protein 135, 268
DVU0328 glycosyl transferase group 1 family protein 14, 135
DVU0423 universal stress protein 60, 109
DVU0490 None 60, 136
DVU0565 gap-1 glyceraldehyde 3-phosphate dehydrogenase 60, 71
DVU0566 GAF domain-containing protein 60, 71
DVU0570 hypothetical protein DVU0570 135, 233
DVU0677 transglycosylase 135, 272
DVU0691 hypothetical protein DVU0691 14, 135
DVU0699 None 14, 135
DVU0773 hypothetical protein DVU0773 60, 157
DVU0881 fusA elongation factor G 60, 115
DVU0882 hypothetical protein DVU0882 53, 60
DVU0883 glutaredoxin 60, 148
DVU0974 hypothetical protein DVU0974 60, 132
DVU0979 dihydroxyacetone kinase subunit DhaK 60, 348
DVU0995 ThiJ/PfpI family protein 60, 153
DVU1004 hypothetical protein DVU1004 14, 135
DVU1283 galU UTP-glucose-1-phosphate uridylyltransferase 60, 249
DVU1397 bfr bacterioferritin 60, 274
DVU1422 OmpA family protein 60, 115
DVU1440 rnc ribonuclease III 135, 272
DVU1528 cytidine/deoxycytidylate deaminase family protein 60, 71
DVU1529 decarboxylase 60, 71
DVU1532 coaD phosphopantetheine adenylyltransferase 135, 336
DVU1541 hypothetical protein DVU1541 60, 115
DVU1548 OmpP1/FadL/TodX family outer membrane transporter 135, 268
DVU1606 TrkA family potassium uptake protein 135, 330
DVU2212 hypothetical protein DVU2212 60, 132
DVU2251 DNA-binding protein 135, 146
DVU2349 carbohydrate phosphorylase family protein 60, 192
DVU2373 OMP85 family outer membrane protein 98, 135
DVU2427 hypothetical protein DVU2427 60, 71
DVU2609 chemotaxis MotB protein 16, 135
DVU2747 hypothetical protein DVU2747 135, 272
DVU2779 ABC transporter solute-binding protein 14, 135
DVU2933 response regulator/sensory box/HDIG domain-containing protein 135, 272
DVU3016 B12 binding /radical SAM domain-containing protein 135, 272
DVU3042 lipoprotein 60, 274
DVU3127 pqiB paraquat-inducible protein B 14, 135
DVU3183 rbO desulfoferrodoxin 60, 348
DVU3184 rubredoxin 60, 348
DVU3185 roO rubredoxin-oxygen oxidoreductase 60, 348
DVU3293 acetolactate synthase 60, 348
DVU3355 SPFH domain-containing protein/band 7 family protein 60, 268
DVU3392 glnA glutamine synthetase, type I 60, 135
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.

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.

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
Comments for DVU3392
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

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