Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3389 topA

DNA topoisomerase I

CircVis
Functional Annotations (7)
Function System
Topoisomerase IA cog/ cog
DNA topoisomerase type I activity go/ molecular_function
chromosome go/ cellular_component
DNA topological change go/ biological_process
DNA unwinding involved in replication go/ biological_process
DNA modification go/ biological_process
topA_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3389
(Mouseover regulator name to see its description)

DVU3389 is regulated by 24 influences and regulates 0 modules.
Regulators for DVU3389 topA (24)
Regulator Module Operator
DVU0309
DVU0653
223 combiner
DVU0653 223 tf
DVU1561
DVU1964
223 combiner
DVU1788
DVU2275
223 combiner
DVU1949 223 tf
DVU2036
DVU2275
223 combiner
DVU2275 223 tf
DVU2557
DVU2195
223 combiner
DVU2909
DVU0653
223 combiner
DVU2909
DVU2275
223 combiner
DVU3167 223 tf
DVU1419 228 tf
DVU1547 228 tf
DVU1788 228 tf
DVU1949 228 tf
DVU2036
DVU1949
228 combiner
DVU2036
DVU2275
228 combiner
DVU2195 228 tf
DVU2275 228 tf
DVU2547 228 tf
DVU2547
DVU1340
228 combiner
DVU2644 228 tf
DVU2675 228 tf
DVU2909
DVU2275
228 combiner

Warning: DVU3389 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
425 1.20e-02 GggcgcAaGgC
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RegPredict
426 8.40e+03 gGCaTcGtATcgAcGaatCaC
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RegPredict
435 1.00e+02 ATGAaAag
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RegPredict
436 1.20e+03 ttgCgTgTCaAtgAA
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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 DVU3389

DVU3389 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Topoisomerase IA cog/ cog
DNA topoisomerase type I activity go/ molecular_function
chromosome go/ cellular_component
DNA topological change go/ biological_process
DNA unwinding involved in replication go/ biological_process
DNA modification go/ biological_process
topA_bact tigr/ tigrfam
Module neighborhood information for DVU3389

DVU3389 has total of 50 gene neighbors in modules 223, 228
Gene neighbors (50)
Gene Common Name Description Module membership
DVU0114 hisG ATP phosphoribosyltransferase 113, 228
DVU0135 hypothetical protein DVU0135 223, 278
DVU0136 hypothetical protein DVU0136 44, 223
DVU0141 M50 family peptidase 9, 223
DVU0282 mutY A/G-specific adenine glycosylase 46, 228
DVU0323 folD bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase 9, 223
DVU0414 NADP-dependent malic enzyme-like protein 176, 223
DVU0660 phosphodiesterase 223, 278
DVU0671 hypothetical protein DVU0671 228, 230
DVU0724 sodium/alanine symporter family protein 223, 278
DVU0726 tgt queuine tRNA-ribosyltransferase 176, 223
DVU0795 purC phosphoribosylaminoimidazole-succinocarboxamide synthase 176, 223
DVU0796 hisD histidinol dehydrogenase 113, 223
DVU1029 hisC histidinol-phosphate aminotransferase 9, 223
DVU1060 glycosyl transferase group 1 family protein 223, 278
DVU1061 glycosyl transferase group 1 family protein 228, 258
DVU1091 hypothetical protein DVU1091 57, 223
DVU1176 hypothetical protein DVU1176 228, 258
DVU1220 nitroreductase family protein 223, 323
DVU1223 hypothetical protein DVU1223 228, 230
DVU1225 hypothetical protein DVU1225 215, 228
DVU1236 amino acid ABC transporter ATP-binding protein 166, 228
DVU1394 hypothetical protein DVU1394 228, 254
DVU1539 glpX fructose 1,6-bisphosphatase II 139, 228
DVU1540 purU formyltetrahydrofolate deformylase 9, 223
DVU1660 undecaprenyl pyrophosphate phosphatase 166, 228
DVU1693 gltX-1 glutamyl-tRNA synthetase 223, 275
DVU1807 nadC nicotinate-nucleotide pyrophosphorylase 228, 258
DVU1827 diaminopimelate aminotransferase 223, 258
DVU1942 DAK2 and DegV domain-containing protein 223, 228
DVU1978 Na+/H+ antiporter family protein 223, 294
DVU2055 metG methionyl-tRNA synthetase 30, 223
DVU2113 xanthine/uracil permease 228, 306
DVU2210 hypothetical protein 180, 223
DVU2254 thyX FAD-dependent thymidylate synthase 75, 228
DVU2255 ruvB Holliday junction DNA helicase RuvB 75, 228
DVU2259 hypothetical protein DVU2259 228, 258
DVU2260 rrmJ ribosomal RNA large subunit methyltransferase J 228, 258
DVU2376 lysS lysyl-tRNA synthetase 228, 258
DVU2436 hypothetical protein DVU2436 223, 278
DVU2471 oxidoreductase, selenocysteine-containing 63, 223
DVU2493 iron-sulfur cluster-binding protein 185, 223
DVU2521 aroK shikimate kinase 228, 230
DVU2552 gltX glutamyl-tRNA synthetase 113, 223
DVU2892 GTP cyclohydrolase 180, 223
DVU3053 hypothetical protein DVU3053 228, 258
DVU3059 ftsY signal recognition particle-docking protein FtsY 228, 258
DVU3090 OMPP1/FadL/TodX family outer membrane protein 64, 228
DVU3208 membrane protein 62, 223
DVU3389 topA DNA topoisomerase I 223, 228
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 DVU3389
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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