Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1730

DNA-binding protein

CircVis
Functional Annotations (3)
Function System
Plasmid maintenance system antidote protein cog/ cog
sequence-specific DNA binding go/ molecular_function
antidote_HigA tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1730
(Mouseover regulator name to see its description)

DVU1730 is regulated by 23 influences and regulates 34 modules.
Regulators for DVU1730 (23)
Regulator Module Operator
DVU0230 289 tf
DVU0309 289 tf
DVU0529 289 tf
DVU0629 289 tf
DVU1754
DVU2802
289 combiner
DVU1754
DVU2989
289 combiner
DVU1967
DVU2989
289 combiner
DVU2036
DVU2251
289 combiner
DVU2359
DVU2690
289 combiner
DVU2359
DVUA0143
289 combiner
DVU0230 90 tf
DVU0277 90 tf
DVU0596 90 tf
DVU0813 90 tf
DVU1690 90 tf
DVU1788 90 tf
DVU2086 90 tf
DVU2359 90 tf
DVU2359
DVU0525
90 combiner
DVU2547 90 tf
DVU3111 90 tf
DVU3167 90 tf
DVU3381 90 tf

Warning: DVU1730 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
177 2.00e-01 gtataacacta.aTcaagaaa..A
Loader icon
RegPredict
178 1.40e+03 cAataGatgac.Atgaaattc
Loader icon
RegPredict
553 1.00e-06 acatgcaTgacAtAtGct.cc
Loader icon
RegPredict
554 1.80e+01 cggcaTcaagagCAT
Loader icon
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 DVU1730

DVU1730 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Plasmid maintenance system antidote protein cog/ cog
sequence-specific DNA binding go/ molecular_function
antidote_HigA tigr/ tigrfam
Module neighborhood information for DVU1730

DVU1730 has total of 46 gene neighbors in modules 90, 289
Gene neighbors (46)
Gene Common Name Description Module membership
DVU0093 glycosyl transferase domain-containing protein 119, 289
DVU0094 methyl-accepting chemotaxis protein 247, 289
DVU0223 hypothetical protein DVU0223 90, 156
DVU0525 MarR family transcriptional regulator 227, 289
DVU0526 drug resistance transporter 90, 120
DVU0673 hypothetical protein DVU0673 70, 289
DVU0727 hypothetical protein DVU0727 90, 110
DVU0728 hypothetical protein DVU0728 90, 110
DVU0756 hypothetical protein 90, 110
DVU1151 hypothetical protein DVU1151 90, 110
DVU1153 hypothetical protein DVU1153 106, 289
DVU1154 hypothetical protein DVU1154 179, 289
DVU1379 hypothetical protein DVU1379 70, 90
DVU1492 None 90, 156
DVU1628 rpoN RNA polymerase sigma-54 factor 90, 110
DVU1629 yfiA ribosomal subunit interface protein 4, 90
DVU1630 PTS system transporter subunit IIA 90, 330
DVU1641 hypothetical protein DVU1641 156, 289
DVU1642 hypothetical protein DVU1642 156, 289
DVU1710 hypothetical protein DVU1710 90, 210
DVU1729 killer protein 13, 90
DVU1730 DNA-binding protein 90, 289
DVU1821 hypothetical protein DVU1821 13, 289
DVU1822 glutamate synthase, amidotransferase subunit 13, 289
DVU1823 glutamate synthase, iron-sulfur cluster-binding subunit 13, 289
DVU1855 integrase, truncation 90, 227
DVU2001 None 90, 220
DVU2062 ATP-dependent DNA helicase UvrD 203, 289
DVU2072 cheA-3 chemotaxis protein CheA 102, 289
DVU2073 cheY-2 chemotaxis protein CheY 179, 289
DVU2074 chemotaxis protein CheW 100, 289
DVU2190 transcriptional regulator 100, 289
DVU2309 methyl-accepting chemotaxis protein 90, 110
DVU2423 transcriptional regulator 90, 289
DVU2614 hypothetical protein DVU2614 41, 90
DVU2694 hypothetical protein DVU2694 137, 289
DVU2742 livM high-affinity branched chain amino acid ABC transporter permease 156, 289
DVU2744 high-affinity branched-chain amino acid ABC transporter perisplasmic amino acid binding protein 156, 289
DVU2845 HIT family protein 90, 309
DVU2846 hypothetical protein DVU2846 90, 335
DVU3244 hypothetical protein DVU3244 247, 289
DVU3289 hypothetical protein DVU3289 106, 289
DVUA0082 phage integrase family site specific recombinase 44, 289
DVUA0083 hypothetical protein DVUA0083 61, 289
DVUA0084 AbrB family transcriptional regulator 156, 289
DVUA0089 hypothetical protein DVUA0089 90, 247
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 DVU1730
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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