Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0836 trmD

tRNA (guanine-N1)-methyltransferase

CircVis
Functional Annotations (6)
Function System
tRNA-(guanine-N1)-methyltransferase cog/ cog
RNA binding go/ molecular_function
tRNA modification go/ biological_process
tRNA processing go/ biological_process
tRNA (guanine-N1-)-methyltransferase activity go/ molecular_function
trmD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0836
(Mouseover regulator name to see its description)

DVU0836 is regulated by 22 influences and regulates 0 modules.
Regulators for DVU0836 trmD (22)
Regulator Module Operator
DVU0682
DVU2275
188 combiner
DVU1547
DVU0230
188 combiner
DVU1547
DVU3142
188 combiner
DVU1547
DVUA0024
188 combiner
DVU1561 188 tf
DVU2275 188 tf
DVU2532
DVU2275
188 combiner
DVU2547 188 tf
DVU2547
DVU2195
188 combiner
DVU2547
DVU2832
188 combiner
DVU3167
DVU2582
188 combiner
DVU0653
DVU2275
306 combiner
DVU1419 306 tf
DVU1547
DVUA0024
306 combiner
DVU1949 306 tf
DVU2036
DVU2275
306 combiner
DVU2423
DVU2832
306 combiner
DVU2423
DVU3381
306 combiner
DVU2547
DVU2588
306 combiner
DVU2547
DVU2832
306 combiner
DVU2547
DVU3142
306 combiner
DVU3381 306 tf

Warning: DVU0836 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
359 3.00e+01 CtTTtCcgaA
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RegPredict
360 4.30e+04 GCgtaccGCATcggGgCAtCcC
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RegPredict
585 1.50e+02 TaattaA.A.AAggcatGCaAcgC
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RegPredict
586 1.40e+02 GTtGCgTg
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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 DVU0836

DVU0836 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
tRNA-(guanine-N1)-methyltransferase cog/ cog
RNA binding go/ molecular_function
tRNA modification go/ biological_process
tRNA processing go/ biological_process
tRNA (guanine-N1-)-methyltransferase activity go/ molecular_function
trmD tigr/ tigrfam
Module neighborhood information for DVU0836

DVU0836 has total of 51 gene neighbors in modules 188, 306
Gene neighbors (51)
Gene Common Name Description Module membership
DVU0274 hypothetical protein DVU0274 188, 236
DVU0836 trmD tRNA (guanine-N1)-methyltransferase 188, 306
DVU0840 ffh signal recognition particle protein 28, 188
DVU0867 aromatic amino acid decarboxylase 28, 306
DVU0931 thiD phosphomethylpyrimidine kinase 30, 306
DVU0950 hypothetical protein DVU0950 160, 188
DVU0956 rpsF 30S ribosomal protein S6 151, 306
DVU0957 rpsR 30S ribosomal protein S18 10, 188
DVU0958 rplI 50S ribosomal protein L9 186, 188
DVU0959 dnaB replicative DNA helicase 186, 188
DVU0966 amino acid ABC transporter periplasmic amino acid-binding protein 146, 306
DVU1021 hypothetical protein DVU1021 186, 188
DVU1022 SUF system FeS assembly ATPase SufC 186, 188
DVU1046 hypothetical protein DVU1046 195, 306
DVU1049 ABC transporter ATP-binding protein 251, 306
DVU1069 branched chain amino acid ABC transporter permease 221, 306
DVU1237 His/Glu/Gln/Arg/opine ABC transporter permease 166, 306
DVU1249 fabD malonyl CoA-ACP transacylase 64, 306
DVU1270 twitching motility protein 166, 306
DVU1274 hypothetical protein DVU1274 64, 306
DVU1282 glmM phosphoglucosamine mutase 52, 188
DVU1287 reductase, iron-sulfur binding subunit 151, 306
DVU1288 cytochrome c family protein 151, 306
DVU1289 reductase, iron-sulfur binding subunit 151, 306
DVU1411 thiC thiamine biosynthesis protein ThiC 139, 306
DVU1455 hypothetical protein DVU1455 137, 188
DVU1624 kdsA 2-dehydro-3-deoxyphosphooctonate aldolase 188, 292
DVU1625 YrbI family phosphatase 188, 292
DVU1627 ABC transporter ATP-binding protein 188, 330
DVU1635 hypothetical protein DVU1635 174, 188
DVU1746 C-5 cytosine-specific DNA methylase family protein 306, 331
DVU1841 fbp fructose-1,6-bisphosphatase 64, 188
DVU1848 hypothetical protein DVU1848 126, 306
DVU1900 hypothetical protein DVU1900 12, 306
DVU1936 phosphonate ABC transporter ATP-binding protein 75, 306
DVU2113 xanthine/uracil permease 228, 306
DVU2252 dnaA-2 chromosomal replication initiator protein DnaA 188, 206
DVU2285 L-lactate permease family protein 145, 306
DVU2335 hypothetical protein DVU2335 258, 306
DVU2522 hypothetical protein DVU2522 113, 188
DVU2533 pheT phenylalanyl-tRNA synthetase subunit beta 186, 306
DVU2903 HD domain-containing protein 27, 188
DVU2921 rpmG 50S ribosomal protein L33 186, 188
DVU2927 rplL 50S ribosomal protein L7/L12 151, 306
DVU2928 rpoB DNA-directed RNA polymerase subunit beta 151, 306
DVU3070 hypothetical protein DVU3070 163, 188
DVU3071 oxidoreductase 186, 188
DVU3207 RNB-like family protein 188, 278
DVU3253 phenylacetate-coenzyme A ligase 230, 306
DVU3274 hypothetical protein DVU3274 55, 188
DVU3367 aspS aspartyl-tRNA synthetase 113, 188
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 DVU0836
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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