Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3084

transcriptional regulator

CircVis
Functional Annotations (4)
Function System
Predicted transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3084
(Mouseover regulator name to see its description)

DVU3084 is regulated by 27 influences and regulates 12 modules.
Regulators for DVU3084 (27)
Regulator Module Operator
DVU1572 143 tf
DVU1572
DVU2106
143 combiner
DVU1572
DVU2527
143 combiner
DVU1645
DVU0916
143 combiner
DVU1674
DVU2836
143 combiner
DVU1964 143 tf
DVU2686 143 tf
DVU2686
DVU3313
143 combiner
DVU2836 143 tf
DVU2836
DVU1331
143 combiner
DVU3080 143 tf
DVU3186 143 tf
DVU3186
DVU1584
143 combiner
DVU3186
DVU2527
143 combiner
DVU0436 157 tf
DVU0936 157 tf
DVU1144 157 tf
DVU2532 157 tf
DVU2557 157 tf
DVU2577
DVU3186
157 combiner
DVU2686 157 tf
DVU2686
DVU1419
157 combiner
DVU2686
DVU2960
157 combiner
DVU2686
DVU3193
157 combiner
DVU2909 157 tf
DVU3193 157 tf
DVUA0024 157 tf

Warning: DVU3084 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
273 7.90e-03 AAcaTTaGcTTaattAaacT
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RegPredict
274 4.70e-05 TtGactTc..cgcTgaAAtccctt
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RegPredict
299 9.80e+01 TTttTCaaTtTtaTAct
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RegPredict
300 1.80e+03 TgAaacgaGGCagCATCaaccaAT
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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 DVU3084

DVU3084 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted transcriptional regulator cog/ cog
DNA binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
zinc ion binding go/ molecular_function
Module neighborhood information for DVU3084

DVU3084 has total of 47 gene neighbors in modules 143, 157
Gene neighbors (47)
Gene Common Name Description Module membership
DVU0035 hypothetical protein DVU0035 157, 279
DVU0111 response regulator 143, 274
DVU0177 modA molybdenum ABC transporter periplasmic molybdenum-binding protein 157, 298
DVU0240 hypothetical protein DVU0240 157, 245
DVU0246 pyruvate phosphate dikinase PEP/pyruvate binding subunit 6, 157
DVU0454 hypothetical protein DVU0454 63, 157
DVU0459 hypothetical protein DVU0459 143, 157
DVU0500 selB selenocysteine-specific translation elongation factor 157, 255
DVU0773 hypothetical protein DVU0773 60, 157
DVU0853 hypothetical protein DVU0853 157, 194
DVU0880 hypothetical protein DVU0880 56, 143
DVU0893 universal stress protein 157, 298
DVU0975 hypothetical protein DVU0975 6, 157
DVU1006 hypothetical protein DVU1006 157, 215
DVU1144 Cro/CI family transcriptional regulator 143, 283
DVU1175 hypothetical protein DVU1175 143, 308
DVU1177 hypothetical protein DVU1177 157, 215
DVU1178 hypothetical protein DVU1178 30, 157
DVU1179 aor tungsten-containing aldehyde:ferredoxin oxidoreductase 157, 348
DVU1285 response regulator 8, 143
DVU1509 hypothetical protein DVU1509 143, 159
DVU1664 engB ribosome biogenesis GTP-binding protein YsxC 56, 143
DVU1665 aroQ 3-dehydroquinate dehydratase 56, 143
DVU1674 transcriptional regulator 156, 157
DVU1675 hypothetical protein DVU1675 156, 157
DVU1758 lipoprotein 143, 283
DVU1834 pyruvate carboxylase 143, 232
DVU1849 pcm protein-L-isoaspartate O-methyltransferase 143, 171
DVU2300 hypothetical protein DVU2300 56, 143
DVU2340 His/Glu/Gln/Arg/opine ABC transporter permease 56, 143
DVU2415 hypothetical protein DVU2415 143, 170
DVU2428 lipoprotein 123, 157
DVU2451 L-lactate permease family protein 157, 263
DVU2523 lipoprotein 157, 166
DVU2655 D-alanyl-D-alanine carboxypeptidase 16, 143
DVU2788 ArsR family transcriptional regulator 6, 157
DVU2912 rpmE 50S ribosomal protein L31 143, 297
DVU3054 radical SAM domain-containing protein 56, 143
DVU3083 hypothetical protein DVU3083 157, 279
DVU3084 transcriptional regulator 143, 157
DVU3089 hypothetical protein DVU3089 143, 339
DVU3150 rpsA 30S ribosomal protein S1 56, 143
DVU3193 DNA-binding protein 157, 206
DVU3228 cheY-3 chemotaxis protein CheY 157, 332
DVU3238 response regulator 146, 157
DVU3240 M24/M37 family peptidase 17, 143
DVU3328 hypothetical protein DVU3328 143, 170
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 DVU3084
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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