Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3095

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 DVU3095
(Mouseover regulator name to see its description)

DVU3095 is regulated by 24 influences and regulates 9 modules.
Regulators for DVU3095 (24)
Regulator Module Operator
DVU0594 216 tf
DVU0594
DVU3186
216 combiner
DVU1964 216 tf
DVU2114
DVU1063
216 combiner
DVU2114
DVU1142
216 combiner
DVU2527 216 tf
DVU2799 216 tf
DVU2886 216 tf
DVU2886
DVU2832
216 combiner
DVU3186
DVU2633
216 combiner
DVU3334
DVU2832
216 combiner
DVU0606 17 tf
DVU0606
DVU1340
17 combiner
DVU0606
DVU2960
17 combiner
DVU0946
DVU2960
17 combiner
DVU1730 17 tf
DVU2527
DVU3080
17 combiner
DVU2799 17 tf
DVU2886 17 tf
DVU2886
DVU2832
17 combiner
DVU2886
DVU3334
17 combiner
DVU2886
DVUA0100
17 combiner
DVU3334
DVUA0100
17 combiner
DVUA0100
DVU2832
17 combiner

Warning: DVU3095 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
33 3.80e-05 tatcAGtAATagtTacTgtTaact
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RegPredict
34 1.50e+02 aacTccTtgcgctt.ctCa
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RegPredict
411 0.00e+00 atAtcAg.Aat.gtT..tgt
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RegPredict
412 3.60e+01 at.TcCTTtCg.tgtttcaa
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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 DVU3095

DVU3095 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 DVU3095

DVU3095 has total of 41 gene neighbors in modules 17, 216
Gene neighbors (41)
Gene Common Name Description Module membership
DVU0024 hypothetical protein DVU0024 17, 216
DVU0033 isochorismatase family protein 122, 216
DVU0151 HAMP domain/sigma-54 interaction domain-containing protein 17, 99
DVU0155 type I phosphodiesterase/nucleotide pyrophosphatase family protein 17, 267
DVU0158 hypothetical protein DVU0158 17, 78
DVU0460 fructose-bisphosphate aldolase 17, 206
DVU0461 3-dehydroquinate synthase 17, 206
DVU0594 iciA chromosome replication initiation inhibitor protein 17, 53
DVU0606 ArsR family transcriptional regulator 206, 216
DVU0607 ahcY S-adenosyl-L-homocysteine hydrolase 206, 216
DVU0685 phosphomannomutase 17, 260
DVU0711 hypothetical protein DVU0711 17, 330
DVU0771 fused molybdenum-pterin binding domain-containing protein/site-specific recombinase phage integrase family 17, 269
DVU0772 hypothetical protein DVU0772 17, 216
DVU0903 HD domain-containing protein 17, 198
DVU0924 rumA 23S rRNA (uracil-5-)-methyltransferase RumA 216, 291
DVU0943 hypothetical protein DVU0943 54, 216
DVU0971 molybdenum cofactor biosynthesis protein 17, 161
DVU0997 metF 5,10-methylenetetrahydrofolate reductase 206, 216
DVU1170 hypothetical protein DVU1170 216, 315
DVU1228 tpX thiol peroxidase 31, 216
DVU1677 tpiA triosephosphate isomerase 17, 230
DVU2230 deoD purine nucleoside phosphorylase 17, 78
DVU2239 glycosy hydrolase family protein 17, 277
DVU2241 pdxA pyridoxal phosphate biosynthetic protein PdxA 17, 216
DVU2246 S1 RNA-binding domain-containing protein 17, 283
DVU2247 anti-oxidant AhpCTSA family protein 17, 216
DVU2248 hypothetical protein DVU2248 17, 216
DVU2318 rubrerythrin 17, 216
DVU2407 hypothetical protein DVU2407 216, 255
DVU2462 oligopeptide ABC transporter permease 17, 161
DVU2672 hypothetical protein DVU2672 17, 179
DVU3093 rdl rubredoxin-like protein 17, 216
DVU3094 rr rubrerythrin 17, 216
DVU3095 Fur family transcriptional regulator 17, 216
DVU3096 hypothetical protein DVU3096 17, 334
DVU3188 NLP/P60 family protein 53, 216
DVU3240 M24/M37 family peptidase 17, 143
DVU3270 cydB cytochrome d ubiquinol oxidase subunit II 17, 216
DVU3271 cydA cytochrome d ubiquinol oxidase subunit I 17, 216
DVU3330 hypothetical protein DVU3330 17, 34
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 DVU3095
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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