Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1089 alaS

alanyl-tRNA synthetase

CircVis
Functional Annotations (8)
Function System
Alanyl-tRNA synthetase cog/ cog
nucleic acid binding go/ molecular_function
alanine-tRNA ligase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
alanyl-tRNA aminoacylation go/ biological_process
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
alaS tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1089
(Mouseover regulator name to see its description)

DVU1089 is regulated by 23 influences and regulates 0 modules.
Regulators for DVU1089 alaS (23)
Regulator Module Operator
DVU0653
DVU2275
323 combiner
DVU0744
DVU0230
323 combiner
DVU0744
DVU2690
323 combiner
DVU1547 323 tf
DVU1561 323 tf
DVU2275 323 tf
DVU2423 323 tf
DVU3167
DVU2582
323 combiner
DVUA0151 323 tf
DVU0653
DVU2275
288 combiner
DVU0744
DVU2832
288 combiner
DVU0936 288 tf
DVU0946
DVU2275
288 combiner
DVU1584
DVU2275
288 combiner
DVU1690 288 tf
DVU2036
DVU2275
288 combiner
DVU2036
DVU2582
288 combiner
DVU2547
DVU2086
288 combiner
DVU2588 288 tf
DVU2588
DVU1547
288 combiner
DVU2836 288 tf
DVU3167
DVU3255
288 combiner
DVU3381 288 tf

Warning: DVU1089 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
551 8.60e-01 ATtgccAaaatTGataTaTagcaa
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RegPredict
552 4.10e+00 AccaGaA.GcgccccacggCgcaA
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RegPredict
615 1.40e+01 CCGcA.ACaCGgGCG
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RegPredict
616 1.90e+01 aTgtCcagAcaaGgtgaTgggtG
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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 DVU1089

DVU1089 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Alanyl-tRNA synthetase cog/ cog
nucleic acid binding go/ molecular_function
alanine-tRNA ligase activity go/ molecular_function
ATP binding go/ molecular_function
cytoplasm go/ cellular_component
alanyl-tRNA aminoacylation go/ biological_process
Aminoacyl-tRNA biosynthesis kegg/ kegg pathway
alaS tigr/ tigrfam
Module neighborhood information for DVU1089

DVU1089 has total of 35 gene neighbors in modules 288, 323
Gene neighbors (35)
Gene Common Name Description Module membership
DVU0064 hypothetical protein DVU0064 5, 323
DVU0165 oligopeptide/dipeptide ABC transporter ATP-binding protein 288, 347
DVU0166 oligopeptide/dipeptide ABC transporter ATP-binding protein 288, 347
DVU0167 oligopeptide/dipeptide ABC transporter permease 288, 347
DVU0168 oligopeptide/dipeptide ABC transporter permease 288, 347
DVU0384 flr flavoredoxin 288, 347
DVU0386 amino acid ABC transporter periplasmic amino acid-binding protein 262, 288
DVU0387 His/Glu/Gln/Arg/opine ABC transporter permease 113, 288
DVU0388 amino acid ABC transporter ATP-binding protein 237, 288
DVU0390 glycolate oxidase subunit GlcD 288, 347
DVU0732 valS valyl-tRNA synthetase 128, 323
DVU1025 upp uracil phosphoribosyltransferase 323, 344
DVU1038 hisA 1-(5-phosphoribosyl)-5- 146, 288
DVU1089 alaS alanyl-tRNA synthetase 288, 323
DVU1090 recA recombinase A 63, 323
DVU1205 acpP acyl carrier protein 169, 323
DVU1206 fabG 3-oxoacyl-ACP reductase 169, 323
DVU1220 nitroreductase family protein 223, 323
DVU1260 outer membrane protein P1 288, 344
DVU1293 None 151, 323
DVU1351 MarC membrane protein 187, 288
DVU1615 paaK-2 phenylacetate-coenzyme A ligase 146, 323
DVU1616 hypothetical protein DVU1616 63, 323
DVU1617 nitroreductase family protein 5, 323
DVU1618 iojap-like protein 5, 323
DVU1619 gpmA phosphoglyceromutase 5, 323
DVU1620 hypothetical protein DVU1620 282, 323
DVU1819 secD preprotein translocase subunit SecD 237, 323
DVU2586 ABC transporter ATP-binding protein 230, 323
DVU2890 hypothetical protein DVU2890 282, 323
DVU3065 AMP-binding protein 81, 323
DVUA0069 GtrA family protein, selenocysteine-containing 288, 347
DVUA0070 hypothetical protein DVUA0070 288, 347
DVUA0074 sulfotransferase family protein 98, 288
DVUA0076 ABC transporter ATP-binding protein 163, 288
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 DVU1089
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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