Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1744

DNA-binding protein

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

Cytoscape Web
Regulation information for DVU1744
(Mouseover regulator name to see its description)

DVU1744 is regulated by 17 influences and regulates 30 modules.
Regulators for DVU1744 (17)
Regulator Module Operator
DVU0594 181 tf
DVU0594
DVU0749
181 combiner
DVU1518
DVU2527
181 combiner
DVU1754
DVU2527
181 combiner
DVU2527
DVU3066
181 combiner
DVU2644
DVU0539
181 combiner
DVU2644
DVU1561
181 combiner
DVU2953 181 tf
DVU1517
DVU0539
33 combiner
DVU1754
DVU2111
33 combiner
DVU2036
DVU2097
33 combiner
DVU2036
DVU2633
33 combiner
DVU2788
DVU2114
33 combiner
DVU2909
DVU1517
33 combiner
DVU3142 33 tf
DVUA0024 33 tf
DVUA0143 33 tf

Warning: DVU1744 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
65 5.10e+02 aTaGgAtAtTTcTT
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RegPredict
66 2.30e+02 tTGtCctttagctTggggtGTgt
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RegPredict
345 5.70e+02 atAAagTCaA.ctaaAAcAcA
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RegPredict
346 1.30e+01 GAcGGcAaggc
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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 DVU1744

DVU1744 is enriched for 1 functions in 2 categories.
Enrichment Table (1)
Function System
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for DVU1744

DVU1744 has total of 55 gene neighbors in modules 33, 181
Gene neighbors (55)
Gene Common Name Description Module membership
DVU0009 TRAP transporter subunit DctM 181, 341
DVU0067 hypothetical protein DVU0067 181, 341
DVU0102 cation ABC transporter periplasmic binding protein 181, 341
DVU0126 ABC transporter ATP-binding protein 33, 181
DVU0249 hypothetical protein DVU0249 69, 181
DVU0308 hypothetical protein DVU0308 181, 280
DVU0324 hypothetical protein DVU0324 9, 181
DVU0346 hypothetical protein DVU0346 162, 181
DVU0363 pabB para-aminobenzoate synthase, component I 181, 334
DVU0541 lipoprotein 33, 285
DVU0736 purN phosphoribosylglycinamide formyltransferase 55, 181
DVU0802 hypothetical protein DVU0802 33, 121
DVU0973 4-hydroxybenzoate octaprenyltransferase 33, 83
DVU0993 hypothetical protein DVU0993 33, 121
DVU1037 mercuric reductase 181, 192
DVU1056 cobalt ABC transporter ATP-binding protein 33, 327
DVU1150 hypothetical protein DVU1150 33, 334
DVU1172 hypothetical protein DVU1172 33, 174
DVU1173 mviN-1 integral membrane protein MviN 33, 181
DVU1280 hypothetical protein DVU1280 33, 330
DVU1347 M24/M37 family peptidase 33, 327
DVU1604 hypothetical protein DVU1604 37, 181
DVU1662 permease 154, 181
DVU1683 hypothetical protein DVU1683 181, 318
DVU1744 DNA-binding protein 33, 181
DVU1762 hypothetical protein DVU1762 33, 343
DVU1857 methyl-accepting chemotaxis protein 33, 122
DVU1908 pdxJ pyridoxine 5'-phosphate synthase 33, 150
DVU1934 phosphonate ABC transporter permease 33, 262
DVU2060 hypothetical protein DVU2060 33, 71
DVU2087 hypothetical protein DVU2087 33, 196
DVU2088 hypothetical protein DVU2088 33, 53
DVU2306 phosphate transporter family protein 33, 154
DVU2358 hypothetical protein DVU2358 181, 275
DVU2447 hypothetical protein DVU2447 33, 81
DVU2618 hypothetical protein DVU2618 35, 181
DVU2627 hypothetical protein DVU2627 14, 33
DVU2700 hypothetical protein DVU2700 33, 69
DVU2730 tail fiber protein 181, 247
DVU2743 livH high-affinity branched-chain amino acid ABC ransporter, permease 181, 275
DVU2761 hypothetical protein DVU2761 181, 214
DVU2787 hypothetical protein DVU2787 48, 181
DVU2823 TRAP transporter subunit DctMQ 69, 181
DVU2871 minor capsid protein C 181, 341
DVU2949 hypothetical protein DVU2949 33, 334
DVU3038 hypothetical protein DVU3038 33, 121
DVU3039 hypothetical protein DVU3039 33, 343
DVU3040 hypothetical protein DVU3040 69, 181
DVU3043 hypothetical protein DVU3043 181, 334
DVU3081 hypothetical protein DVU3081 181, 341
DVU3108 nhaC-2 Na+/H+ antiporter NhaC 181, 341
DVU3115 hypothetical protein DVU3115 33, 334
DVU3175 hypothetical protein DVU3175 33, 327
DVU3180 GGDEF domain-containing protein 33, 87
DVU3267 hypothetical protein DVU3267 181, 341
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 DVU1744
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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