Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0334

D-alanine--D-alanine ligase

CircVis
Functional Annotations (10)
Function System
D-alanine-D-alanine ligase and related ATP-grasp enzymes cog/ cog
ATP binding go/ molecular_function
cell wall go/ cellular_component
cytoplasm go/ cellular_component
D-alanine-D-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
D-Alanine metabolism kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
D_ala_D_alaTIGR tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0334
(Mouseover regulator name to see its description)

DVU0334 is regulated by 20 influences and regulates 0 modules.
Regulators for DVU0334 (20)
Regulator Module Operator
DVU0230 63 tf
DVU0749
DVU0539
63 combiner
DVU0749
DVU3334
63 combiner
DVU0749
DVUA0024
63 combiner
DVU2036
DVU1144
63 combiner
DVU2114 63 tf
DVU2527
DVU0653
63 combiner
DVU2836
DVU0569
63 combiner
DVU2836
DVU1788
63 combiner
DVU2836
DVU3193
63 combiner
DVU0529
DVU0539
195 combiner
DVU0653 195 tf
DVU0653
DVU2275
195 combiner
DVU0946 195 tf
DVU3167 195 tf
DVU3167
DVU0269
195 combiner
DVU3381
DVU2832
195 combiner
DVUA0057 195 tf
DVUA0151 195 tf
DVUA0151
DVU1561
195 combiner

Warning: DVU0334 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
123 1.20e+00 aaGacaCcAcAgGAtAGGAa
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RegPredict
124 3.90e+02 gGAGgCATGAC
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RegPredict
373 3.10e-03 ATacaagAcAaGgtTtTccTga
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RegPredict
374 1.90e+02 TTcgTtgcagagGgc
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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 DVU0334

DVU0334 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
D-alanine-D-alanine ligase and related ATP-grasp enzymes cog/ cog
ATP binding go/ molecular_function
cell wall go/ cellular_component
cytoplasm go/ cellular_component
D-alanine-D-alanine ligase activity go/ molecular_function
peptidoglycan biosynthetic process go/ biological_process
D-Alanine metabolism kegg/ kegg pathway
Peptidoglycan biosynthesis kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
D_ala_D_alaTIGR tigr/ tigrfam
Module neighborhood information for DVU0334

DVU0334 has total of 50 gene neighbors in modules 63, 195
Gene neighbors (50)
Gene Common Name Description Module membership
DVU0034 DSBA-like thioredoxin domain-containing protein 50, 63
DVU0056 cheV-1 chemotaxis protein CheV 63, 343
DVU0227 hypothetical protein DVU0227 63, 255
DVU0334 D-alanine--D-alanine ligase 63, 195
DVU0395 HIT family protein 63, 194
DVU0454 hypothetical protein DVU0454 63, 157
DVU0575 hypothetical protein DVU0575 63, 226
DVU0619 sigma-54 dependent transcriptional regulator 63, 198
DVU0620 L-PSP family endoribonuclease 63, 214
DVU0656 hypothetical protein DVU0656 63, 303
DVU0698 rfbC dTDP-4-dehydrorhamnose 3,5-epimerase 171, 195
DVU0854 NirD protein 63, 226
DVU0951 molybdopterin biosynthesis MoeA protein 50, 195
DVU1017 ABC transporter ATP-binding protein/permease 54, 195
DVU1018 HlyD family type I secretion membrane fusion protein 54, 195
DVU1043 guaA GMP synthase 64, 195
DVU1046 hypothetical protein DVU1046 195, 306
DVU1090 recA recombinase A 63, 323
DVU1339 lipoprotein 195, 275
DVU1340 Fur family transcriptional regulator 195, 275
DVU1341 cation ABC transporter permease 195, 275
DVU1342 cation ABC transporter ATP-binding protein 195, 275
DVU1343 cation ABC transporter periplasmc-binding protein 195, 275
DVU1344 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 166, 195
DVU1345 proS prolyl-tRNA synthetase 195, 275
DVU1346 xseA exodeoxyribonuclease VII large subunit 75, 195
DVU1349 geranylgeranyl diphosphate synthase 75, 195
DVU1350 dxs 1-deoxy-D-xylulose-5-phosphate synthase 195, 275
DVU1408 hypothetical protein DVU1408 63, 196
DVU1434 hypothetical protein DVU1434 57, 63
DVU1537 lipoprotein 63, 297
DVU1579 cysS cysteinyl-tRNA synthetase 63, 282
DVU1616 hypothetical protein DVU1616 63, 323
DVU1820 yajC preprotein translocase, YajC subunit 63, 297
DVU1877 polysaccharide deacetylase family protein 63, 215
DVU1888 ATP-NAD kinase domain-containing protein 63, 128
DVU2275 sigma-54 dependent transcriptional regulator 113, 195
DVU2425 rarD rarD protein 141, 195
DVU2471 oxidoreductase, selenocysteine-containing 63, 223
DVU2612 hypothetical protein DVU2612 63, 249
DVU2638 hypothetical protein DVU2638 83, 195
DVU2639 hypothetical protein DVU2639 57, 63
DVU2644 GntR family transcriptional regulator 63, 230
DVU2783 hypothetical protein DVU2783 146, 195
DVU3011 hypothetical protein DVU3011 176, 195
DVU3281 hypothetical protein DVU3281 52, 63
DVU3345 None 63, 120
DVU3359 hypothetical protein DVU3359 57, 63
DVU3379 ribonucleotide-diphosphate reductase subunit alpha 172, 195
DVUA0111 type III secretion system protein IpaC family 136, 195
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 DVU0334
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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