Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2333 ndk

nucleoside diphosphate kinase

CircVis
Functional Annotations (10)
Function System
Nucleoside diphosphate kinase cog/ cog
nucleoside diphosphate kinase activity go/ molecular_function
ATP binding go/ molecular_function
GTP biosynthetic process go/ biological_process
UTP biosynthetic process go/ biological_process
CTP biosynthetic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2333
(Mouseover regulator name to see its description)

DVU2333 is regulated by 26 influences and regulates 0 modules.
Regulators for DVU2333 ndk (26)
Regulator Module Operator
DVU1547 64 tf
DVU1547
DVU0230
64 combiner
DVU1547
DVUA0024
64 combiner
DVU1584
DVU2275
64 combiner
DVU2195 64 tf
DVU2547
DVU1419
64 combiner
DVU2547
DVU2588
64 combiner
DVU2588 64 tf
DVU0277 226 tf
DVU0679
DVU0110
226 combiner
DVU0749 226 tf
DVU0813 226 tf
DVU0813
DVU1745
226 combiner
DVU1063 226 tf
DVU1547
DVU0110
226 combiner
DVU1628 226 tf
DVU1788 226 tf
DVU2086 226 tf
DVU2086
DVU2909
226 combiner
DVU2527 226 tf
DVU2567
DVU1628
226 combiner
DVU2567
DVU2644
226 combiner
DVU2644 226 tf
DVU2644
DVU1063
226 combiner
DVU3111 226 tf
DVUA0024
DVU0110
226 combiner

Warning: DVU2333 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
125 6.50e+01 ACCGCaAtAtcAaGgAaagag
Loader icon
RegPredict
126 2.90e+02 TtccgT.gacgCGtGccGTgcg
Loader icon
RegPredict
431 2.00e+00 AtggtcaAacaaAAa
Loader icon
RegPredict
432 2.80e+03 ACaGGACGC.T
Loader icon
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 DVU2333

DVU2333 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Nucleoside diphosphate kinase cog/ cog
nucleoside diphosphate kinase activity go/ molecular_function
ATP binding go/ molecular_function
GTP biosynthetic process go/ biological_process
UTP biosynthetic process go/ biological_process
CTP biosynthetic process go/ biological_process
Purine metabolism kegg/ kegg pathway
Pyrimidine metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for DVU2333

DVU2333 has total of 48 gene neighbors in modules 64, 226
Gene neighbors (48)
Gene Common Name Description Module membership
DVU0002 dnaN DNA polymerase III subunit beta 29, 64
DVU0003 gyrB DNA gyrase subunit B 29, 64
DVU0285 hisH imidazole glycerol phosphate synthase subunit HisH 44, 64
DVU0359 HesB-like domain-containing protein 119, 226
DVU0389 His/Glu/Gln/Arg/opine amino acid ABC transporter permease 217, 226
DVU0501 hypothetical protein DVU0501 64, 221
DVU0505 truB tRNA pseudouridine synthase B 44, 64
DVU0574 None 226, 254
DVU0575 hypothetical protein DVU0575 63, 226
DVU0830 ptsH phosphocarrier protein HPr 64, 166
DVU0831 PTS system transporter subunit IID 64, 119
DVU0832 tetrapyrrole methylase family protein 215, 226
DVU0854 NirD protein 63, 226
DVU0866 dxr 1-deoxy-D-xylulose 5-phosphate reductoisomerase 110, 226
DVU1042 tatB twin-arginine translocation protein TatB 64, 113
DVU1043 guaA GMP synthase 64, 195
DVU1078 R3H domain-containing protein 10, 64
DVU1249 fabD malonyl CoA-ACP transacylase 64, 306
DVU1250 gidB methyltransferase GidB 64, 313
DVU1274 hypothetical protein DVU1274 64, 306
DVU1380 hypothetical protein DVU1380 57, 226
DVU1381 hypothetical protein DVU1381 57, 226
DVU1382 HesB family selenoprotein 167, 226
DVU1567 hypothetical protein DVU1567 226, 337
DVU1577 hslV ATP-dependent protease peptidase subunit 12, 226
DVU1578 hypothetical protein 215, 226
DVU1644 permease 110, 226
DVU1645 ArsR family transcriptional regulator 110, 226
DVU1680 suhB inositol-1-monophosphatase 12, 226
DVU1745 DNA-binding protein 226, 233
DVU1841 fbp fructose-1,6-bisphosphatase 64, 188
DVU1943 hypothetical protein DVU1943 167, 226
DVU1975 methyl-accepting chemotaxis protein 226, 239
DVU1985 hypothetical protein DVU1985 196, 226
DVU2225 acetyl-CoA carboxylase, carboxyl transferase, alpha/subunit beta 64, 78
DVU2332 proC pyrroline-5-carboxylate reductase 64, 318
DVU2333 ndk nucleoside diphosphate kinase 64, 226
DVU2536 rpmI 50S ribosomal protein L35 64, 186
DVU2621 hypothetical protein DVU2621 57, 226
DVU2662 hypothetical protein DVU2662 110, 226
DVU2785 GntR family transcriptional regulator 160, 226
DVU2904 ribosomal RNA large subunit methyltransferase N 5, 64
DVU2941 hypothetical protein DVU2941 215, 226
DVU3090 OMPP1/FadL/TodX family outer membrane protein 64, 228
DVU3242 rpoZ DNA-directed RNA polymerase subunit omega 226, 267
DVU3245 greA transcription elongation factor GreA 64, 226
DVU3357 hypothetical protein DVU3357 57, 226
DVU3358 ParA family protein 57, 226
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 DVU2333
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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