Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU2111

LysR family transcriptional regulator

CircVis
Functional Annotations (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU2111
(Mouseover regulator name to see its description)

DVU2111 is regulated by 19 influences and regulates 11 modules.
Regulators for DVU2111 (19)
Regulator Module Operator
DVU0629 25 tf
DVU0653
DVU2251
25 combiner
DVU0936 25 tf
DVU1754 25 tf
DVU1754
DVU2319
25 combiner
DVU2114
DVU0569
25 combiner
DVU2557
DVU2251
25 combiner
DVU2567 25 tf
DVU2909
DVU3142
25 combiner
DVU0277 160 tf
DVU0379
DVU1517
160 combiner
DVU0379
DVU1561
160 combiner
DVU0379
DVU2567
160 combiner
DVU0804
DVU1517
160 combiner
DVU1754 160 tf
DVU1967 160 tf
DVU3023
DVU0569
160 combiner
DVU3023
DVU1745
160 combiner
DVU3167
DVU1744
160 combiner

Warning: DVU2111 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
49 1.50e+00 CA.cCGcCAtc
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RegPredict
50 6.00e+04 AGTTTTT
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RegPredict
305 1.60e+01 gGCgtTGCgGgTgc
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RegPredict
306 2.00e+03 TGTGTTACGAATAATA
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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 DVU2111

DVU2111 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for DVU2111

DVU2111 has total of 43 gene neighbors in modules 25, 160
Gene neighbors (43)
Gene Common Name Description Module membership
DVU0144 cytidyltransferase-like protein 25, 95
DVU0178 None 160, 225
DVU0377 trxB-1 thioredoxin reductase 25, 305
DVU0479 serine/threonine protein kinase 160, 345
DVU0496 polA DNA polymerase I 25, 82
DVU0617 hypothetical protein DVU0617 160, 305
DVU0710 competence protein comM 160, 240
DVU0735 MOSC domain-containing protein 25, 202
DVU0816 cobQ cobyric acid synthase 25, 202
DVU0877 hypothetical protein DVU0877 160, 284
DVU0914 cobS cobalamin-5-phosphate synthase 92, 160
DVU0948 hypothetical protein DVU0948 160, 256
DVU0949 hypothetical protein DVU0949 160, 256
DVU0950 hypothetical protein DVU0950 160, 188
DVU1055 heptosyltransferase family protein 160, 254
DVU1111 hypothetical protein DVU1111 160, 283
DVU1217 MATE efflux family protein 160, 258
DVU1224 nfo endonuclease IV 25, 97
DVU1253 hypothetical protein DVU1253 25, 238
DVU1527 phage integrase family site specific recombinase 25, 265
DVU1659 hypothetical protein DVU1659 160, 239
DVU1763 hypothetical protein DVU1763 25, 261
DVU1804 glycosyl transferase group 1 family protein 25, 260
DVU1899 DNA repair protein RecO 25, 284
DVU1983 hypothetical protein DVU1983 25, 51
DVU2111 LysR family transcriptional regulator 25, 160
DVU2197 phage integrase family site specific recombinase 25, 156
DVU2272 formate acetyltransferase 25, 97
DVU2350 gid tRNA (uracil-5-)-methyltransferase Gid 25, 261
DVU2751 hypothetical protein DVU2751 97, 160
DVU2760 hypothetical protein DVU2760 25, 261
DVU2772 hypothetical protein DVU2772 160, 261
DVU2784 FMN-dependent family dehydrogenase 160, 260
DVU2785 GntR family transcriptional regulator 160, 226
DVU3114 kdsB 3-deoxy-manno-octulosonate cytidylyltransferase 25, 315
DVU3130 hypothetical protein DVU3130 140, 160
DVU3170 cobJ precorrin-3b C17-methyltransferase 25, 97
DVU3237 phosphoenolpyruvate synthase-like protein 160, 291
DVU3241 hypothetical protein DVU3241 160, 305
DVU3317 hypothetical protein DVU3317 25, 70
DVU3377 dgkA diacylglycerol kinase 25, 238
DVU3394 hypothetical protein DVU3394 25, 238
DVUA0106 YopN family type III secretion target protein 25, 131
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 DVU2111
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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