Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1340

Fur family transcriptional regulator

CircVis
Functional Annotations (3)
Function System
Fe2+/Zn2+ uptake regulation proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1340
(Mouseover regulator name to see its description)

DVU1340 is regulated by 19 influences and regulates 18 modules.
Regulators for DVU1340 (19)
Regulator Module Operator
DVU0529
DVU0539
195 combiner
DVU0653 195 tf
DVU0653
DVU2275
195 combiner
DVU0946 195 tf
DVU3167 195 tf
DVU3167
DVU0269
195 combiner
DVU3381
DVU2832
195 combiner
DVUA0057 195 tf
DVUA0151 195 tf
DVUA0151
DVU1561
195 combiner
DVU0653 275 tf
DVU0749 275 tf
DVU1518
DVU0936
275 combiner
DVU1690
DVU0529
275 combiner
DVU2547
DVU1547
275 combiner
DVU2577
DVU0936
275 combiner
DVU2989 275 tf
DVU3084
DVU0529
275 combiner
DVUA0151
DVU3084
275 combiner

Warning: DVU1340 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
373 3.10e-03 ATacaagAcAaGgtTtTccTga
Loader icon
RegPredict
374 1.90e+02 TTcgTtgcagagGgc
Loader icon
RegPredict
525 1.50e+00 AaaaCcTtGtcTttTAT
Loader icon
RegPredict
526 2.70e+01 GaATccgGCAAcC
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 DVU1340

DVU1340 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Fe2+/Zn2+ uptake regulation proteins cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for DVU1340

DVU1340 has total of 36 gene neighbors in modules 195, 275
Gene neighbors (36)
Gene Common Name Description Module membership
DVU0334 D-alanine--D-alanine ligase 63, 195
DVU0698 rfbC dTDP-4-dehydrorhamnose 3,5-epimerase 171, 195
DVU0951 molybdopterin biosynthesis MoeA protein 50, 195
DVU1017 ABC transporter ATP-binding protein/permease 54, 195
DVU1018 HlyD family type I secretion membrane fusion protein 54, 195
DVU1043 guaA GMP synthase 64, 195
DVU1046 hypothetical protein DVU1046 195, 306
DVU1262 twitching motility protein PilT 260, 275
DVU1339 lipoprotein 195, 275
DVU1340 Fur family transcriptional regulator 195, 275
DVU1341 cation ABC transporter permease 195, 275
DVU1342 cation ABC transporter ATP-binding protein 195, 275
DVU1343 cation ABC transporter periplasmc-binding protein 195, 275
DVU1344 ispG 4-hydroxy-3-methylbut-2-en-1-yl diphosphate synthase 166, 195
DVU1345 proS prolyl-tRNA synthetase 195, 275
DVU1346 xseA exodeoxyribonuclease VII large subunit 75, 195
DVU1348 xseB exodeoxyribonuclease VII small subunit 275, 298
DVU1349 geranylgeranyl diphosphate synthase 75, 195
DVU1350 dxs 1-deoxy-D-xylulose-5-phosphate synthase 195, 275
DVU1693 gltX-1 glutamyl-tRNA synthetase 223, 275
DVU2256 ruvA Holliday junction DNA helicase RuvA 94, 275
DVU2275 sigma-54 dependent transcriptional regulator 113, 195
DVU2284 hypothetical protein DVU2284 5, 275
DVU2358 hypothetical protein DVU2358 181, 275
DVU2418 vanZ-like family protein 83, 275
DVU2425 rarD rarD protein 141, 195
DVU2594 hypothetical protein DVU2594 69, 275
DVU2613 hypothetical protein DVU2613 55, 275
DVU2638 hypothetical protein DVU2638 83, 195
DVU2660 hypothetical protein DVU2660 69, 275
DVU2743 livH high-affinity branched-chain amino acid ABC ransporter, permease 181, 275
DVU2783 hypothetical protein DVU2783 146, 195
DVU3011 hypothetical protein DVU3011 176, 195
DVU3250 hypothetical protein DVU3250 142, 275
DVU3379 ribonucleotide-diphosphate reductase subunit alpha 172, 195
DVUA0111 type III secretion system protein IpaC family 136, 195
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 DVU1340
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