Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0004 gyrA

DNA gyrase subunit A

CircVis
Functional Annotations (7)
Function System
Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit cog/ cog
DNA topoisomerase (ATP-hydrolyzing) activity go/ molecular_function
ATP binding go/ molecular_function
chromosome go/ cellular_component
DNA topological change go/ biological_process
DNA unwinding involved in replication go/ biological_process
gyrA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0004
(Mouseover regulator name to see its description)

DVU0004 is regulated by 23 influences and regulates 0 modules.
Regulators for DVU0004 gyrA (23)
Regulator Module Operator
DVU0744
DVU0230
18 combiner
DVU0744
DVU3142
18 combiner
DVU0936
DVU2275
18 combiner
DVU1144 18 tf
DVU1156 18 tf
DVU1547 18 tf
DVU1572
DVU1690
18 combiner
DVU1690 18 tf
DVU1690
DVU2582
18 combiner
DVU2423
DVU0619
18 combiner
DVU2532
DVU2275
18 combiner
DVU3255
DVU1144
18 combiner
DVU0063 29 tf
DVU0682 29 tf
DVU0682
DVU3255
29 combiner
DVU1547
DVU3142
29 combiner
DVU1572
DVU3255
29 combiner
DVU1949 29 tf
DVU2275
DVU1949
29 combiner
DVU2423 29 tf
DVU2547
DVU2588
29 combiner
DVU2547
DVU3142
29 combiner
DVU3255
DVU1690
29 combiner

Warning: DVU0004 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
35 1.50e+00 ttgaaga.cAaaAaaagAaAG
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RegPredict
36 1.60e+04 TAAAGTaTACA
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RegPredict
57 6.70e-01 aCaccGAAgaGAA.a
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RegPredict
58 3.20e+04 AaCaTAAAcTATA
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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 DVU0004

DVU0004 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit cog/ cog
DNA topoisomerase (ATP-hydrolyzing) activity go/ molecular_function
ATP binding go/ molecular_function
chromosome go/ cellular_component
DNA topological change go/ biological_process
DNA unwinding involved in replication go/ biological_process
gyrA tigr/ tigrfam
Module neighborhood information for DVU0004

DVU0004 has total of 42 gene neighbors in modules 18, 29
Gene neighbors (42)
Gene Common Name Description Module membership
DVU0002 dnaN DNA polymerase III subunit beta 29, 64
DVU0003 gyrB DNA gyrase subunit B 29, 64
DVU0004 gyrA DNA gyrase subunit A 18, 29
DVU0161 purF amidophosphoribosyltransferase 10, 29
DVU0162 carB carbamoyl-phosphate synthase large subunit 10, 29
DVU0237 serS seryl-tRNA synthetase 29, 176
DVU0279 sulfate permease family protein 29, 347
DVU0502 hypothetical protein DVU0502 29, 56
DVU0563 ISD1, transposase OrfB 18, 121
DVU0809 gatC glutamyl-tRNA(Gln) amidotransferase subunit C 29, 235
DVU0810 hypothetical protein DVU0810 29, 235
DVU0835 rplS 50S ribosomal protein L19 18, 297
DVU0837 rimM 16S rRNA processing protein RimM 18, 232
DVU0838 hypothetical protein DVU0838 18, 232
DVU0839 rpsP 30S ribosomal protein S16 18, 297
DVU0927 rplU 50S ribosomal protein L21 18, 297
DVU0928 rpmA 50S ribosomal protein L27 18, 297
DVU1033 competence/damage-inducible protein CinA protein, truncation 18, 78
DVU1062 hypothetical protein DVU1062 12, 29
DVU1074 rpmH 50S ribosomal protein L34 18, 78
DVU1195 lipoprotein 29, 169
DVU1248 argS arginyl-tRNA synthetase 29, 235
DVU1257 RNA-binding protein 18, 263
DVU1302 rpsJ 30S ribosomal protein S10 18, 212
DVU1334 tig trigger factor 18, 297
DVU1576 ispE 4-diphosphocytidyl-2-C-methyl-D-erythritol kinase 29, 56
DVU1584 sigma 70 family protein 29, 282
DVU1661 hypothetical protein DVU1661 29, 331
DVU1666 efp elongation factor P 29, 56
DVU1676 secG preprotein translocase subunit SecG 18, 297
DVU1792 rpsU 30S ribosomal protein S21 18, 297
DVU1889 gmhA phosphoheptose isomerase 29, 128
DVU1893 ATP-dependent protease 29, 78
DVU1931 iron-sulfur cluster-binding protein 18, 98
DVU2215 RNA-binding protein 18, 171
DVU2222 ssb single-strand binding protein 18, 78
DVU2339 ribosomal protein L11 methyltransferase 29, 75
DVU2538 thrS threonyl-tRNA synthetase 18, 292
DVU2920 tuf elongation factor Tu 18, 297
DVU3275 hypothetical protein DVU3275 29, 337
DVU3307 ubiX 3-octaprenyl-4-hydroxybenzoate carboxy-lyase 29, 235
DVU3395 M24/M37 family peptidase 29, 179
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 DVU0004
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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