Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU0856 hemB

delta-aminolevulinic acid dehydratase

CircVis
Functional Annotations (7)
Function System
Delta-aminolevulinic acid dehydratase cog/ cog
porphobilinogen synthase activity go/ molecular_function
tetrapyrrole biosynthetic process go/ biological_process
metal ion binding go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU0856
(Mouseover regulator name to see its description)

DVU0856 is regulated by 25 influences and regulates 0 modules.
Regulators for DVU0856 hemB (25)
Regulator Module Operator
DVU0277 227 tf
DVU0277
DVU0916
227 combiner
DVU0619
DVU0230
227 combiner
DVU0744
DVU2690
227 combiner
DVU0813
DVU0230
227 combiner
DVU2086
DVU0744
227 combiner
DVU2547
DVU0230
227 combiner
DVU2567 227 tf
DVU2567
DVU0813
227 combiner
DVU2909
DVU1730
227 combiner
DVU2909
DVU2690
227 combiner
DVU0110 57 tf
DVU0309 57 tf
DVU0619 57 tf
DVU0813 57 tf
DVU0813
DVU0230
57 combiner
DVU0813
DVU1745
57 combiner
DVU0854 57 tf
DVU0854
DVU3111
57 combiner
DVU1518
DVU0813
57 combiner
DVU1628
DVU0813
57 combiner
DVU1788 57 tf
DVU2086 57 tf
DVU2567
DVU0813
57 combiner
DVU2644 57 tf

Warning: DVU0856 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
111 2.40e-01 caCcaccGatGttatAcGGaAagC
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RegPredict
112 1.40e+02 TtgTC.GGGGTgGC
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RegPredict
433 4.10e+03 CTGCTGaCGatG
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RegPredict
434 8.30e+03 AtcatCGcctt
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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 DVU0856

DVU0856 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Delta-aminolevulinic acid dehydratase cog/ cog
porphobilinogen synthase activity go/ molecular_function
tetrapyrrole biosynthetic process go/ biological_process
metal ion binding go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
Module neighborhood information for DVU0856

DVU0856 has total of 50 gene neighbors in modules 57, 227
Gene neighbors (50)
Gene Common Name Description Module membership
DVU0159 thioesterase family protein 57, 119
DVU0160 carbohydrate isomerase KpsF/GutQ family protein 57, 119
DVU0243 lipoprotein 57, 119
DVU0417 speA arginine decarboxylase 57, 119
DVU0483 DNA mismatch repair protein MutL 4, 57
DVU0525 MarR family transcriptional regulator 227, 289
DVU0759 M29 family peptidase 13, 227
DVU0801 uvrC excinuclease ABC subunit C 57, 110
DVU0825 secA preprotein translocase subunit SecA 218, 227
DVU0855 radical SAM domain-containing protein 57, 198
DVU0856 hemB delta-aminolevulinic acid dehydratase 57, 227
DVU0864 glycoprotease family protein 57, 227
DVU0865 membrane-associated zinc metalloprotease 158, 227
DVU0982 hypothetical protein DVU0982 57, 211
DVU0985 hypothetical protein DVU0985 57, 110
DVU0989 periplasmic divalent cation tolerance protein cutA 57, 99
DVU1091 hypothetical protein DVU1091 57, 223
DVU1191 ATP-dependent protease La 57, 227
DVU1193 radC DNA repair protein RadC 57, 227
DVU1267 hypothetical protein DVU1267 158, 227
DVU1380 hypothetical protein DVU1380 57, 226
DVU1381 hypothetical protein DVU1381 57, 226
DVU1383 hypothetical protein DVU1383 57, 167
DVU1401 hypothetical protein DVU1401 57, 211
DVU1432 radical SAM domain-containing protein 57, 227
DVU1434 hypothetical protein DVU1434 57, 63
DVU1466 argB acetylglutamate kinase 13, 57
DVU1467 hslU ATP-dependent protease ATP-binding subunit HslU 119, 227
DVU1580 ribose 5-phosphate isomerase 57, 294
DVU1788 rpoD RNA polymerase sigma-70 factor 28, 227
DVU1789 dnaG DNA primase 28, 227
DVU1855 integrase, truncation 90, 227
DVU2261 hypothetical protein DVU2261 57, 309
DVU2363 thiM hydroxyethylthiazole kinase 66, 227
DVU2487 hypothetical protein DVU2487 66, 227
DVU2488 hypothetical protein DVU2488 66, 227
DVU2554 hypothetical protein DVU2554 119, 227
DVU2621 hypothetical protein DVU2621 57, 226
DVU2639 hypothetical protein DVU2639 57, 63
DVU2909 MarR family transcriptional regulator 57, 261
DVU3202 TatD family hydrolase 57, 261
DVU3243 dnaJ chaperone protein DnaJ 28, 227
DVU3283 hypothetical protein DVU3283 4, 57
DVU3314 U32 family peptidase 57, 100
DVU3315 pyrK dihydroorotate dehydrogenase, electron transfer subunit 66, 227
DVU3357 hypothetical protein DVU3357 57, 226
DVU3358 ParA family protein 57, 226
DVU3359 hypothetical protein DVU3359 57, 63
DVU3365 fmt methionyl-tRNA formyltransferase 28, 227
DVU3366 def polypeptide deformylase 227, 261
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 DVU0856
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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