Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1142

transcriptional regulator

CircVis
Functional Annotations (1)
Function System
DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1142
(Mouseover regulator name to see its description)

DVU1142 is regulated by 23 influences and regulates 11 modules.
Regulators for DVU1142 (23)
Regulator Module Operator
DVU0118 269 tf
DVU1547
DVU2894
269 combiner
DVU1949 269 tf
DVU2195
DVU1730
269 combiner
DVU2423 269 tf
DVU2547 269 tf
DVU2547
DVU1547
269 combiner
DVU2894
DVU3381
269 combiner
DVU0230 231 tf
DVU0539 231 tf
DVU0679
DVU0525
231 combiner
DVU0679
DVU2690
231 combiner
DVU0916
DVU2835
231 combiner
DVU1572
DVU2835
231 combiner
DVU2195 231 tf
DVU2527
DVU2114
231 combiner
DVU2582
DVU2251
231 combiner
DVU2644
DVU2114
231 combiner
DVU2827 231 tf
DVU2836
DVU2275
231 combiner
DVU3080 231 tf
DVU3305
DVU0230
231 combiner
DVUA0151 231 tf

Warning: DVU1142 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
441 4.30e+02 TccAagCatcAggaGgCTtT
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RegPredict
442 2.90e+03 TAcTAcCCACTGAACCCCTTCaA
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RegPredict
513 2.70e+03 aAATGaacTtTctcactgaaACA
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RegPredict
514 6.40e+03 AaATcAtAta..CcgaCAtcgaAa
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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 DVU1142

DVU1142 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
DNA binding go/ molecular_function
Module neighborhood information for DVU1142

DVU1142 has total of 35 gene neighbors in modules 231, 269
Gene neighbors (35)
Gene Common Name Description Module membership
DVU0244 hypothetical protein DVU0244 26, 269
DVU0573 creA creA protein 115, 269
DVU0589 molybdopterin-guanine dinucleotide biosynthesis protein MobB/FeS domain-containing protein protein 178, 269
DVU0771 fused molybdenum-pterin binding domain-containing protein/site-specific recombinase phage integrase family 17, 269
DVU0981 multiphosphoryl transfer protein 109, 269
DVU1116 hypothetical protein DVU1116 24, 231
DVU1117 hypothetical protein DVU1117 208, 231
DVU1118 hypothetical protein DVU1118 24, 231
DVU1120 hypothetical protein DVU1120 24, 231
DVU1128 lysozyme 231, 341
DVU1129 hypothetical protein DVU1129 231, 341
DVU1131 hypothetical protein DVU1131 231, 322
DVU1135 hypothetical protein DVU1135 24, 231
DVU1136 host-nuclease inhibitor protein Gam 112, 231
DVU1139 bacteriophage DNA transposition B protein 183, 231
DVU1141 hypothetical protein DVU1141 54, 231
DVU1142 transcriptional regulator 231, 269
DVU1143 hypothetical protein DVU1143 24, 231
DVU1545 hemolysin-type calcium-binding repeat/calx-beta domain-containing protein 269, 313
DVU1800 None 269, 296
DVU1973 rhodanese-like domain-containing protein 269, 274
DVU2245 mutT/nudix family protein 269, 296
DVU2408 hypothetical protein DVU2408 69, 269
DVU2687 hypothetical protein DVU2687 247, 269
DVU2688 bacteriophage transposase A protein 182, 231
DVU2698 lipoprotein 231, 322
DVU2699 transglycosylase 231, 330
DVU2711 major head subunit 231, 276
DVU2712 hypothetical protein DVU2712 138, 231
DVU2714 hypothetical protein DVU2714 182, 231
DVU3076 hypothetical protein DVU3076 269, 274
DVU3077 AhpC/TSA family protein 192, 269
DVU3123 HD domain-containing protein 254, 269
DVU3124 hypothetical protein DVU3124 34, 269
DVU3393 hypothetical protein DVU3393 123, 269
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 DVU1142
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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