Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1964

Rrf2 family transcriptional regulator

CircVis
Functional Annotations (2)
Function System
Predicted transcriptional regulator cog/ cog
rrf2_super tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1964
(Mouseover regulator name to see its description)

DVU1964 is regulated by 22 influences and regulates 14 modules.
Regulators for DVU1964 (22)
Regulator Module Operator
DVU0539 219 tf
DVU0916
DVU1744
219 combiner
DVU1331
DVU0916
219 combiner
DVU1572
DVU1744
219 combiner
DVU1760 219 tf
DVU2114 219 tf
DVU2275 219 tf
DVU2690 219 tf
DVU3080
DVU1760
219 combiner
DVU3313 219 tf
DVU0539 170 tf
DVU0916 170 tf
DVU1572 170 tf
DVU1572
DVU2106
170 combiner
DVU1628 170 tf
DVU1645
DVU3313
170 combiner
DVU2114 170 tf
DVU2675 170 tf
DVU2956 170 tf
DVU3080 170 tf
DVU3313 170 tf
DVU3313
DVU2106
170 combiner

Warning: DVU1964 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
325 0.00e+00 aAaaatTca.aatcttctTccAat
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RegPredict
326 2.70e-05 AaATCAtaaaaAaAtTcCAAACAG
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RegPredict
417 1.20e-01 aAagctagcagACattgTGCttT
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RegPredict
418 6.70e-01 Aaa.aAtCTtT
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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 DVU1964

DVU1964 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Predicted transcriptional regulator cog/ cog
rrf2_super tigr/ tigrfam
Module neighborhood information for DVU1964

DVU1964 has total of 44 gene neighbors in modules 170, 219
Gene neighbors (44)
Gene Common Name Description Module membership
DVU0163 lipoprotein 170, 279
DVU0369 hypothetical protein DVU0369 170, 263
DVU0604 hypothetical protein DVU0604 170, 283
DVU0695 None 126, 219
DVU0781 hypothetical protein DVU0781 126, 219
DVU0782 hypothetical protein DVU0782 126, 219
DVU0783 hypothetical protein DVU0783 12, 219
DVU1010 hypothetical protein DVU1010 170, 179
DVU1015 hypothetical protein DVU1015 8, 170
DVU1082 3' exoribonuclease family protein 219, 282
DVU1155 hypothetical protein DVU1155 8, 170
DVU1277 hypothetical protein DVU1277 170, 339
DVU1393 hypothetical protein DVU1393 126, 219
DVU1478 hypothetical protein DVU1478 170, 233
DVU1637 hypothetical protein DVU1637 8, 170
DVU1638 hypothetical protein DVU1638 8, 170
DVU1639 hypothetical protein DVU1639 8, 170
DVU1678 rimI ribosomal-protein-alanine acetyltransferase 219, 279
DVU1760 TetR family transcriptional regulator 170, 279
DVU1859 hypothetical protein DVU1859 187, 219
DVU1905 hypothetical protein DVU1905 170, 279
DVU1964 Rrf2 family transcriptional regulator 170, 219
DVU1965 hypothetical protein DVU1965 170, 219
DVU1966 hypothetical protein DVU1966 187, 219
DVU2017 ISDvu5, transposase 121, 219
DVU2066 phage integrase family site specific recombinase 219, 308
DVU2067 GGDEF domain-containing protein 219, 342
DVU2145 chloramphenicol acetyltransferase 8, 170
DVU2146 hypothetical protein DVU2146 8, 170
DVU2182 hypothetical protein DVU2182 170, 263
DVU2183 hypothetical protein DVU2183 170, 263
DVU2229 motA-2 chemotaxis protein MotA 78, 170
DVU2265 hypothetical protein DVU2265 219, 330
DVU2415 hypothetical protein DVU2415 143, 170
DVU2648 hypothetical protein DVU2648 219, 279
DVU2651 hypothetical protein DVU2651 219, 263
DVU2652 hypothetical protein DVU2652 179, 219
DVU2653 hypothetical protein DVU2653 179, 219
DVU2827 sigma-54 dependent transcriptional regulator 170, 339
DVU2917 lpxC UDP-3-O- 113, 219
DVU2919 hypothetical protein DVU2919 170, 219
DVU3138 hypothetical protein DVU3138 121, 219
DVU3146 hypothetical protein DVU3146 219, 308
DVU3328 hypothetical protein DVU3328 143, 170
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 DVU1964
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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