Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1613

glutamate synthase subunit beta

CircVis
Functional Annotations (10)
Function System
NADPH-dependent glutamate synthase beta chain and related oxidoreductases cog/ cog
glutamate synthase (NADPH) activity go/ molecular_function
electron transport go/ biological_process
glutamate synthase complex (NADPH) go/ cellular_component
glutamate synthase (NADH) activity go/ molecular_function
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1613
(Mouseover regulator name to see its description)

DVU1613 is regulated by 30 influences and regulates 0 modules.
Regulators for DVU1613 (30)
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
DVU0030 236 tf
DVU0110
DVU0813
236 combiner
DVU0110
DVU1083
236 combiner
DVU0110
DVU1419
236 combiner
DVU0619 236 tf
DVU0653
DVU0813
236 combiner
DVU1584 236 tf
DVU1645
DVU2644
236 combiner
DVU1744 236 tf
DVU2423
DVU0653
236 combiner
DVU2423
DVU0936
236 combiner
DVU2644
DVU3066
236 combiner
DVU2836 236 tf
DVU3167 236 tf
DVU3167
DVU0309
236 combiner
DVU3167
DVU0813
236 combiner
DVU3193
DVU0813
236 combiner

Warning: DVU1613 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
367 1.00e-02 gGcttTGGCGT
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RegPredict
368 4.20e+02 GCAtCGcAtgt
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RegPredict
451 2.90e+02 AgTcaTc.CATTtTT
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RegPredict
452 7.90e+03 CatcActggaGgAA
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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 DVU1613

DVU1613 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
NADPH-dependent glutamate synthase beta chain and related oxidoreductases cog/ cog
glutamate synthase (NADPH) activity go/ molecular_function
electron transport go/ biological_process
glutamate synthase complex (NADPH) go/ cellular_component
glutamate synthase (NADH) activity go/ molecular_function
Alanine aspartate and glutamate metabolism kegg/ kegg pathway
Nitrogen metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Microbial metabolism in diverse environments kegg/ kegg pathway
Module neighborhood information for DVU1613

DVU1613 has total of 67 gene neighbors in modules 192, 236
Gene neighbors (67)
Gene Common Name Description Module membership
DVU0090 wcaG GDP-fucose synthetase 137, 236
DVU0175 tungsten formylmethanofuran dehydrogenase family protein/molybdopterin binding protein 192, 348
DVU0274 hypothetical protein DVU0274 188, 236
DVU0290 lipoprotein 115, 236
DVU0322 eno phosphopyruvate hydratase 229, 236
DVU0378 thioredoxin 137, 236
DVU0398 HMGL-like domain-containing protein 236, 292
DVU0418 lys1 saccharopine dehydrogenase 119, 236
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
DVU0761 lipoprotein 35, 236
DVU0870 frr ribosome recycling factor 27, 236
DVU1037 mercuric reductase 181, 192
DVU1072 hypothetical protein DVU1072 99, 236
DVU1368 rhodanese-like domain-containing protein 35, 236
DVU1396 hypothetical protein DVU1396 192, 274
DVU1412 glycerate dehydrogenase 236, 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
DVU1868 dapA dihydrodipicolinate synthase 62, 236
DVU1886 hypothetical protein DVU1886 128, 236
DVU1958 sensory box histidine kinase 69, 192
DVU1980 hypothetical protein DVU1980 115, 236
DVU1986 hypothetical protein DVU1986 192, 198
DVU2082 flagellin 62, 236
DVU2108 hypothetical protein DVU2108 66, 236
DVU2109 hypothetical protein DVU2109 236, 348
DVU2112 hypothetical protein DVU2112 27, 236
DVU2143 fba fructose-1,6-bisphosphate aldolase, class II 186, 236
DVU2203 L-PSP family endoribonuclease 62, 236
DVU2313 pgl 6-phosphogluconolactonase 115, 236
DVU2349 carbohydrate phosphorylase family protein 60, 192
DVU2360 FAD/NAD-binding family oxidoreductase 115, 192
DVU2420 hypothetical protein DVU2420 119, 236
DVU2421 4-oxalocrotonate tautomerase family protein 192, 274
DVU2422 nitroreductase family protein 192, 274
DVU2460 hypothetical protein DVU2460 229, 236
DVU2482 fdnG-2 formate dehydrogenase subunit alpha, selenocysteine-containing 192, 348
DVU2490 histidinol phosphatase 35, 236
DVU2735 paaK-3 phenylacetate-coenzyme A ligase 62, 236
DVU2769 hypothetical protein DVU2769 27, 236
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
DVU3212 pyridine nucleotide-disulfide oxidoreductase 5, 236
DVU3217 hypothetical protein DVU3217 109, 192
DVU3282 ADP-ribosylglycohydrolase family protein 109, 192
DVU3351 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase 50, 236
DVU3352 lipoprotein 27, 236
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.

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 DVU1613
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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