Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2904

ribosomal RNA large subunit methyltransferase N

CircVis
Functional Annotations (7)
Function System
Predicted Fe-S-cluster redox enzyme cog/ cog
structural constituent of ribosome go/ molecular_function
catalytic activity go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
iron-sulfur cluster binding go/ molecular_function
TIGR00048 tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2904
(Mouseover regulator name to see its description)

DVU2904 is regulated by 21 influences and regulates 0 modules.
Regulators for DVU2904 (21)
Regulator Module Operator
DVU1561
DVU0118
5 combiner
DVU1572
DVU2423
5 combiner
DVU1572
DVU3313
5 combiner
DVU1730 5 tf
DVU1745 5 tf
DVU1759 5 tf
DVU1759
DVU2275
5 combiner
DVU2111
DVU1964
5 combiner
DVU2275 5 tf
DVU2275
DVU0057
5 combiner
DVU2423
DVU3313
5 combiner
DVU2557 5 tf
DVU2989 5 tf
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

Warning: DVU2904 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
9 6.40e+00 cTtgtttG.AAG.gaaTaaat.ga
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RegPredict
10 2.30e+03 CtCACaCCACAaAC
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RegPredict
125 6.50e+01 ACCGCaAtAtcAaGgAaagag
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RegPredict
126 2.90e+02 TtccgT.gacgCGtGccGTgcg
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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 DVU2904

DVU2904 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Predicted Fe-S-cluster redox enzyme cog/ cog
structural constituent of ribosome go/ molecular_function
catalytic activity go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
iron-sulfur cluster binding go/ molecular_function
TIGR00048 tigr/ tigrfam
Module neighborhood information for DVU2904

DVU2904 has total of 55 gene neighbors in modules 5, 64
Gene neighbors (55)
Gene Common Name Description Module membership
DVU0002 dnaN DNA polymerase III subunit beta 29, 64
DVU0003 gyrB DNA gyrase subunit B 29, 64
DVU0036 hypothetical protein DVU0036 5, 103
DVU0052 era GTP-binding protein Era 5, 30
DVU0057 TetR family transcriptional regulator 5, 316
DVU0060 RND family efflux transporter MFP subunit 5, 94
DVU0061 multidrug resistance protein 5, 94
DVU0062 RND efflux system outer membrane lipoprotein 5, 94
DVU0063 MarR family transcriptional regulator 5, 94
DVU0064 hypothetical protein DVU0064 5, 323
DVU0085 trpB-1 tryptophan synthase subunit beta 5, 95
DVU0285 hisH imidazole glycerol phosphate synthase subunit HisH 44, 64
DVU0501 hypothetical protein DVU0501 64, 221
DVU0505 truB tRNA pseudouridine synthase B 44, 64
DVU0602 hypothetical protein DVU0602 5, 179
DVU0603 hypothetical protein DVU0603 5, 94
DVU0830 ptsH phosphocarrier protein HPr 64, 166
DVU0831 PTS system transporter subunit IID 64, 119
DVU0872 glycosyl transferase group 2 family protein 5, 55
DVU1009 hypothetical protein DVU1009 5, 30
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
DVU1454 ispD 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase 5, 278
DVU1571 rho transcription termination factor Rho 5, 235
DVU1617 nitroreductase family protein 5, 323
DVU1618 iojap-like protein 5, 323
DVU1619 gpmA phosphoglyceromutase 5, 323
DVU1841 fbp fructose-1,6-bisphosphatase 64, 188
DVU1851 M24/M37 family peptidase 5, 16
DVU2130 hypothetical protein DVU2130 5, 94
DVU2148 hypothetical protein DVU2148 5, 316
DVU2208 hypothetical protein DVU2208 5, 179
DVU2225 acetyl-CoA carboxylase, carboxyl transferase, alpha/subunit beta 64, 78
DVU2274 hypothetical protein DVU2274 5, 44
DVU2284 hypothetical protein DVU2284 5, 275
DVU2299 glycine/betaine/L-proline ABC transporter ATP binding protein 5, 235
DVU2332 proC pyrroline-5-carboxylate reductase 64, 318
DVU2333 ndk nucleoside diphosphate kinase 64, 226
DVU2536 rpmI 50S ribosomal protein L35 64, 186
DVU2634 hypothetical protein DVU2634 5, 9
DVU2671 phosphodiesterase 5, 121
DVU2904 ribosomal RNA large subunit methyltransferase N 5, 64
DVU3090 OMPP1/FadL/TodX family outer membrane protein 64, 228
DVU3151 tRNA modifying protein 5, 94
DVU3194 engA GTP-binding protein EngA 5, 94
DVU3204 purA adenylosuccinate synthetase 5, 94
DVU3205 transglycosylase 5, 94
DVU3206 phosphoribosylaminoimidazolecarboxamide formyltransferase 5, 235
DVU3212 pyridine nucleotide-disulfide oxidoreductase 5, 236
DVU3245 greA transcription elongation factor GreA 64, 226
DVU3313 LysR family transcriptional regulator 5, 279
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 DVU2904
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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