Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1709 hsdM

type I restriction-modification system, M subunit

CircVis
Functional Annotations (6)
Function System
Type I restriction-modification system methyltransferase subunit cog/ cog
DNA binding go/ molecular_function
DNA methylation go/ biological_process
N-methyltransferase activity go/ molecular_function
site-specific DNA-methyltransferase (adenine-specific) activity go/ molecular_function
hsdM tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1709
(Mouseover regulator name to see its description)

DVU1709 is regulated by 22 influences and regulates 0 modules.
Regulators for DVU1709 hsdM (22)
Regulator Module Operator
DVU0110 215 tf
DVU0936 215 tf
DVU1144 215 tf
DVU1645
DVU2644
215 combiner
DVU1690
DVU0942
215 combiner
DVU2275 215 tf
DVU2319 215 tf
DVU2644 215 tf
DVU2686 215 tf
DVU3334
DVU0110
215 combiner
DVU0230 244 tf
DVU0653 244 tf
DVU1063 244 tf
DVU1517 244 tf
DVU1518
DVU2195
244 combiner
DVU1561 244 tf
DVU1754 244 tf
DVU1754
DVU0030
244 combiner
DVU2567 244 tf
DVU2788
DVU0653
244 combiner
DVU3023
DVU0110
244 combiner
DVU3167 244 tf

Warning: DVU1709 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
409 5.00e+00 GtATAGattaAaT.TaT..aT
Loader icon
RegPredict
410 3.90e+02 T.TTgAcaaT.AT.tGtgaTtA
Loader icon
RegPredict
465 0.00e+00 TgaTaa.cTcaAcAAAAAacGagG
Loader icon
RegPredict
466 5.10e-03 aaGtcaagcgcc.TCaAGAGa
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 DVU1709

DVU1709 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Type I restriction-modification system methyltransferase subunit cog/ cog
DNA binding go/ molecular_function
DNA methylation go/ biological_process
N-methyltransferase activity go/ molecular_function
site-specific DNA-methyltransferase (adenine-specific) activity go/ molecular_function
hsdM tigr/ tigrfam
Module neighborhood information for DVU1709

DVU1709 has total of 47 gene neighbors in modules 215, 244
Gene neighbors (47)
Gene Common Name Description Module membership
DVU0023 hypothetical protein DVU0023 215, 283
DVU0225 hypothetical protein DVU0225 215, 255
DVU0702 cytochrome c family protein 215, 255
DVU0715 branched-chain amino acid ABC transporter ATP binding protein 215, 331
DVU0716 branched-chain amino acid ABC transporter ATP-binding protein 215, 331
DVU0745 ABC transporter periplasmic substrate-binding protein 215, 230
DVU0832 tetrapyrrole methylase family protein 215, 226
DVU0909 hypothetical protein DVU0909 92, 244
DVU0915 hypothetical protein DVU0915 12, 244
DVU0920 atpI ATP synthase protein I 2, 244
DVU0921 5-nitroimidazole antibiotic resistance protein 70, 244
DVU0926 hypothetical protein DVU0926 133, 244
DVU0929 obgE GTPase ObgE 133, 244
DVU0965 hypothetical protein DVU0965 146, 215
DVU1006 hypothetical protein DVU1006 157, 215
DVU1098 adenine specific DNA methyltransferase 118, 244
DVU1177 hypothetical protein DVU1177 157, 215
DVU1225 hypothetical protein DVU1225 215, 228
DVU1232 glnB-1 nitrogen regulatory protein P-II 31, 215
DVU1354 hypothetical protein DVU1354 215, 309
DVU1578 hypothetical protein 215, 226
DVU1588 hpt hypoxanthine phosphoribosyltransferase 215, 294
DVU1669 rluB ribosomal large subunit pseudouridine synthase B 215, 337
DVU1707 hypothetical protein DVU1707 243, 244
DVU1708 hypothetical protein DVU1708 215, 244
DVU1709 hsdM type I restriction-modification system, M subunit 215, 244
DVU1736 hypothetical protein DVU1736 86, 244
DVU1873 ppiB-2 peptidyl-prolyl cis-trans isomerase B 215, 254
DVU1877 polysaccharide deacetylase family protein 63, 215
DVU1988 hypothetical protein DVU1988 224, 244
DVU2198 hypothetical protein DVU2198 244, 263
DVU2206 hypothetical protein DVU2206 78, 215
DVU2235 hypothetical protein DVU2235 215, 308
DVU2249 hypothetical protein DVU2249 3, 244
DVU2250 AMP-binding protein 86, 244
DVU2296 mtgA monofunctional biosynthetic peptidoglycan transglycosylase 3, 244
DVU2308 hypothetical protein DVU2308 215, 332
DVU2527 transcriptional regulator 215, 224
DVU2645 Na+/H+ antiporter family protein 80, 244
DVU2646 D-cysteine desulfhydrase 20, 244
DVU2657 6-pyruvoyl tetrahydrobiopterin synthase 215, 279
DVU2658 hypothetical protein DVU2658 119, 215
DVU2659 exsB protein 119, 215
DVU2778 hypothetical protein DVU2778 215, 263
DVU2831 hypothetical protein DVU2831 84, 244
DVU2940 hypothetical protein DVU2940 146, 215
DVU2941 hypothetical protein DVU2941 215, 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 DVU1709
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