Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0990

endonuclease III

CircVis
Functional Annotations (8)
Function System
Predicted EndoIII-related endonuclease cog/ cog
DNA-(apurinic or apyrimidinic site) lyase activity go/ molecular_function
endonuclease activity go/ molecular_function
intracellular go/ cellular_component
base-excision repair go/ biological_process
4 iron, 4 sulfur cluster binding go/ molecular_function
Base excision repair kegg/ kegg pathway
nth tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0990
(Mouseover regulator name to see its description)

DVU0990 is regulated by 21 influences and regulates 0 modules.
Regulators for DVU0990 (21)
Regulator Module Operator
DVU0110
DVU0569
23 combiner
DVU0230 23 tf
DVU0309
DVU0653
23 combiner
DVU0653 23 tf
DVU1561 23 tf
DVU1754
DVU1561
23 combiner
DVU3167 23 tf
DVU3167
DVU0309
23 combiner
DVU3167
DVU0569
23 combiner
DVU3167
DVU3305
23 combiner
DVU3167
DVUA0100
23 combiner
DVUA0024 23 tf
DVU1628
DVU1964
65 combiner
DVU1949 65 tf
DVU2675 65 tf
DVU2788
DVU0629
65 combiner
DVU2788
DVU2557
65 combiner
DVU2788
DVU3186
65 combiner
DVU2799
DVU1628
65 combiner
DVU2799
DVU2394
65 combiner
DVU3313 65 tf

Warning: DVU0990 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
45 1.70e+01 atGTGCtGCGgGG
Loader icon
RegPredict
46 6.50e+00 CacatGaCaCagCCG
Loader icon
RegPredict
127 8.30e+00 GaatCGgCatCgtAtgacA
Loader icon
RegPredict
128 3.70e+00 cATgcgGgAtGTtcCgcCggcag
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 DVU0990

DVU0990 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Predicted EndoIII-related endonuclease cog/ cog
DNA-(apurinic or apyrimidinic site) lyase activity go/ molecular_function
endonuclease activity go/ molecular_function
intracellular go/ cellular_component
base-excision repair go/ biological_process
4 iron, 4 sulfur cluster binding go/ molecular_function
Base excision repair kegg/ kegg pathway
nth tigr/ tigrfam
Module neighborhood information for DVU0990

DVU0990 has total of 55 gene neighbors in modules 23, 65
Gene neighbors (55)
Gene Common Name Description Module membership
DVU0084 aIF-2BI family translation initiation factor 9, 23
DVU0182 radical SAM domain-containing protein 65, 254
DVU0286 hisF imidazole glycerol phosphate synthase subunit HisF 15, 65
DVU0333 hypothetical protein DVU0333 65, 137
DVU0348 hypothetical protein DVU0348 23, 250
DVU0487 purE phosphoribosylaminoimidazole carboxylase, catalytic subunit 23, 176
DVU0646 cobI precorrin-2 C20-methyltransferase 23, 176
DVU0647 iron compound ABC transporter periplasmic iron compount-binding protein 23, 211
DVU0648 iron compound ABC transporter ATP-binding protein 23, 176
DVU0649 iron compound ABC transporter permease 23, 176
DVU0650 chelatase 23, 176
DVU0703 lepA GTP-binding protein LepA 28, 65
DVU0843 hypothetical protein DVU0843 23, 137
DVU0868 cdsA phosphatidate cytidylyltransferase 28, 65
DVU0871 pyrH uridylate kinase 28, 65
DVU0988 carbohydrate kinase 23, 65
DVU0990 endonuclease III 23, 65
DVU0991 hypothetical protein DVU0991 23, 65
DVU1039 lipoprotein 23, 180
DVU1040 hisB imidazoleglycerol-phosphate dehydratase 23, 180
DVU1054 HAD superfamily hydrolase 65, 230
DVU1071 hypothetical protein DVU1071 65, 261
DVU1196 leuS leucyl-tRNA synthetase 65, 169
DVU1197 nusB N utilization substance protein B 65, 248
DVU1214 dolichyl-phosphate-mannose-protein mannosyltransferase family protein 65, 294
DVU1215 PAP2 family protein 65, 278
DVU1251 hypothetical protein DVU1251 65, 270
DVU1272 general secretion pathway protein E 65, 221
DVU1273 type II/III secretion system protein 65, 270
DVU1275 hypothetical protein DVU1275 65, 221
DVU1352 6-pyruvoyl tetrahydrobiopterin synthase 65, 291
DVU1353 dnaE DNA polymerase III subunit alpha 65, 172
DVU1395 C4-type zinc finger DksA/TraR family protein 65, 254
DVU1599 crcB crcB protein 65, 337
DVU1621 hypothetical protein DVU1621 28, 65
DVU1878 ltaE threonine aldolase 65, 270
DVU1879 glycosyl transferase group 1 family protein 65, 270
DVU1907 ugd UDP-glucose 6-dehydrogenase 65, 251
DVU1927 ileS isoleucyl-tRNA synthetase 23, 180
DVU1929 hypothetical protein DVU1929 23, 237
DVU1930 hypothetical protein 23, 186
DVU2135 hypothetical protein DVU2135 65, 208
DVU2224 hypothetical protein DVU2224 65, 86
DVU2258 ruvC Holliday junction resolvase 65, 119
DVU2322 UTP--glucose-1-phosphate uridylyltransferase 23, 174
DVU2463 recN DNA repair protein RecN 23, 141
DVU2464 hypothetical protein DVU2464 23, 30
DVU3023 sigma-54 dependent DNA-binding response regulator 23, 214
DVU3066 DNA-binding protein 65, 270
DVU3154 deoxyribonucleotide triphosphate pyrophosphatase 23, 250
DVU3161 ABC transporter ATP-binding protein 23, 300
DVU3168 hemL glutamate-1-semialdehyde aminotransferase 23, 327
DVU3198 DNA polymerase III subunits gamma/tau 23, 180
DVU3199 hypothetical protein DVU3199 23, 220
DVU3200 recR recombination protein RecR 23, 220
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 DVU0990
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