Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3111

Crp/FNR family transcriptional regulator

CircVis
Functional Annotations (0)

Warning: No Functional annotations were found!

GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3111
(Mouseover regulator name to see its description)

DVU3111 is regulated by 18 influences and regulates 16 modules.
Regulators for DVU3111 (18)
Regulator Module Operator
DVU0744
DVU0525
267 combiner
DVU0744
DVU1730
267 combiner
DVU0916
DVU2934
267 combiner
DVU1518
DVU1730
267 combiner
DVU0679 37 tf
DVU0744 37 tf
DVU1063 37 tf
DVU1340 37 tf
DVU1628 37 tf
DVU1949 37 tf
DVU2359 37 tf
DVU2547
DVU2582
37 combiner
DVU2547
DVU3229
37 combiner
DVU2934 37 tf
DVU3111 37 tf
DVU3167 37 tf
DVU3381 37 tf
DVUA0100 37 tf

Warning: DVU3111 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
73 6.10e+03 ATtGCTaTCGT
Loader icon
RegPredict
74 1.60e+04 CAtAtgacAGAaaCC
Loader icon
RegPredict
509 7.30e+01 CgagGcCcacagtgaacGacA
Loader icon
RegPredict
510 2.00e+03 T.tgCccc.CttcaAcGgca
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 DVU3111

Warning: No Functional annotations were found!

Module neighborhood information for DVU3111

DVU3111 has total of 52 gene neighbors in modules 37, 267
Gene neighbors (52)
Gene Common Name Description Module membership
DVU0040 hypothetical protein DVU0040 37, 267
DVU0048 chemotaxis protein MotB 185, 267
DVU0140 response regulator 37, 99
DVU0145 response regulator 37, 205
DVU0147 lipoprotein 37, 53
DVU0155 type I phosphodiesterase/nucleotide pyrophosphatase family protein 17, 267
DVU0218 tail protein 37, 314
DVU0232 hypothetical protein DVU0232 37, 99
DVU0257 acetyltransferase 37, 69
DVU0301 hypothetical protein DVU0301 37, 330
DVU0358 hypothetical protein DVU0358 37, 99
DVU0381 nhaC-1 Na+/H+ antiporter NhaC 37, 341
DVU0392 aromatic aminotransferase 37, 185
DVU0425 hypothetical protein DVU0425 14, 37
DVU0638 hypothetical protein DVU0638 14, 37
DVU0639 pomB chemotaxis protein PomB 37, 205
DVU0641 hypothetical protein DVU0641 37, 225
DVU0791 methylated DNA-protein cysteine methyltransferase DNA binding subunit 247, 267
DVU0818 hypothetical protein DVU0818 185, 267
DVU1011 hypothetical protein DVU1011 37, 245
DVU1014 hypothetical protein DVU1014 267, 331
DVU1031 hypothetical protein DVU1031 224, 267
DVU1126 lipoprotein 37, 267
DVU1227 hypothetical protein DVU1227 267, 296
DVU1360 galE UDP-glucose 4-epimerase 37, 342
DVU1442 flagellin FlaG 37, 286
DVU1604 hypothetical protein DVU1604 37, 181
DVU1691 hypothetical protein DVU1691 37, 44
DVU1731 hypothetical protein DVU1731 31, 267
DVU1906 hypothetical protein DVU1906 37, 313
DVU1939 anaerobic glycerol-3-phosphate dehydrogenase subunit B 198, 267
DVU1993 cation transporter E1-E2 family ATPase 37, 296
DVU2086 GntR family transcriptional regulator 209, 267
DVU2115 hypothetical protein DVU2115 82, 267
DVU2267 hypothetical protein DVU2267 37, 179
DVU2311 None 37, 261
DVU2437 ABC transporter permease 46, 267
DVU2473 hypothetical protein DVU2473 37, 46
DVU2498 hypothetical protein DVU2498 37, 342
DVU2551 HD domain-containing protein 37, 342
DVU2589 hypothetical protein DVU2589 37, 153
DVU2590 sensory box protein 37, 153
DVU2972 chemotaxis protein CheD 37, 274
DVU3021 HDIG domain-containing protein 37, 245
DVU3036 hypothetical protein DVU3036 37, 281
DVU3060 hypothetical protein DVU3060 37, 166
DVU3092 hypothetical protein DVU3092 89, 267
DVU3111 Crp/FNR family transcriptional regulator 37, 267
DVU3225 hypothetical protein DVU3225 37, 198
DVU3242 rpoZ DNA-directed RNA polymerase subunit omega 226, 267
DVU3342 hypothetical protein DVU3342 37, 123
DVU3391 hypothetical protein DVU3391 37, 305
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 DVU3111
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