Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1201 ribD

riboflavin biosynthesis protein RibD

CircVis
Functional Annotations (11)
Function System
Pyrimidine reductase, riboflavin biosynthesis cog/ cog
alcohol dehydrogenase activity, metal ion-independent go/ molecular_function
alcohol dehydrogenase activity, zinc-dependent go/ molecular_function
alcohol dehydrogenase activity, iron-dependent go/ molecular_function
zinc ion binding go/ molecular_function
5-amino-6-(5-phosphoribosylamino)uracil reductase activity go/ molecular_function
diaminohydroxyphosphoribosylaminopyrimidine deaminase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
Riboflavin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
eubact_ribD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1201
(Mouseover regulator name to see its description)

DVU1201 is regulated by 23 influences and regulates 0 modules.
Regulators for DVU1201 ribD (23)
Regulator Module Operator
DVU0118 94 tf
DVU1572
DVU1730
94 combiner
DVU1572
DVU2319
94 combiner
DVU1572
DVU2423
94 combiner
DVU1572
DVU2956
94 combiner
DVU1572
DVU3313
94 combiner
DVU1745 94 tf
DVU1759 94 tf
DVU1759
DVU2275
94 combiner
DVU2111
DVU3186
94 combiner
DVU2275 94 tf
DVU2989 94 tf
DVU3167 94 tf
DVU3305 94 tf
DVU3313 94 tf
DVU0619
DVU0525
169 combiner
DVU0619
DVU3381
169 combiner
DVU0744
DVU0230
169 combiner
DVU1518
DVU2086
169 combiner
DVU2086
DVU2832
169 combiner
DVU2532
DVU0653
169 combiner
DVU3167
DVU0063
169 combiner
DVU3167
DVU1572
169 combiner

Warning: DVU1201 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
181 2.20e-02 ATCGCTtgTatGcaaGTtaaT
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RegPredict
182 1.70e+02 CaTcaACCgga.a.aaggAAca.c
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RegPredict
323 9.00e-06 AAGaGaatGagGtcTtaTaCC
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RegPredict
324 2.90e-04 aAcctGTGCaggGctggcGAcAtg
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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 DVU1201

DVU1201 is enriched for 11 functions in 3 categories.
Enrichment Table (11)
Function System
Pyrimidine reductase, riboflavin biosynthesis cog/ cog
alcohol dehydrogenase activity, metal ion-independent go/ molecular_function
alcohol dehydrogenase activity, zinc-dependent go/ molecular_function
alcohol dehydrogenase activity, iron-dependent go/ molecular_function
zinc ion binding go/ molecular_function
5-amino-6-(5-phosphoribosylamino)uracil reductase activity go/ molecular_function
diaminohydroxyphosphoribosylaminopyrimidine deaminase activity go/ molecular_function
riboflavin biosynthetic process go/ biological_process
Riboflavin metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
eubact_ribD tigr/ tigrfam
Module neighborhood information for DVU1201

DVU1201 has total of 49 gene neighbors in modules 94, 169
Gene neighbors (49)
Gene Common Name Description Module membership
DVU0060 RND family efflux transporter MFP subunit 5, 94
DVU0061 multidrug resistance protein 5, 94
DVU0062 RND efflux system outer membrane lipoprotein 5, 94
DVU0063 MarR family transcriptional regulator 5, 94
DVU0224 hypothetical protein DVU0224 94, 156
DVU0603 hypothetical protein DVU0603 5, 94
DVU1002 hypothetical protein DVU1002 169, 172
DVU1003 dnaJ domain-containing protein 169, 172
DVU1194 hypothetical protein DVU1194 169, 308
DVU1195 lipoprotein 29, 169
DVU1196 leuS leucyl-tRNA synthetase 65, 169
DVU1198 ribH 6,7-dimethyl-8-ribityllumazine synthase 169, 248
DVU1200 ribE riboflavin synthase subunit alpha 169, 308
DVU1201 ribD riboflavin biosynthesis protein RibD 94, 169
DVU1202 cytidine/deoxycytidylate deaminase family protein 10, 169
DVU1203 glyA serine hydroxymethyltransferase 169, 248
DVU1204 fabF 3-oxoacyl-ACP synthase 169, 248
DVU1205 acpP acyl carrier protein 169, 323
DVU1206 fabG 3-oxoacyl-ACP reductase 169, 323
DVU1207 fabH 3-oxoacyl-ACP synthase 10, 169
DVU1209 rpmF 50S ribosomal protein L32 169, 308
DVU1210 hypothetical protein DVU1210 28, 169
DVU1211 rpmB 50S ribosomal protein L28 169, 308
DVU1332 selD selenide, water dikinase, selenocysteine-containing 30, 94
DVU1775 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase 12, 94
DVU1780 hypothetical protein DVU1780 169, 229
DVU1781 hypothetical protein DVU1781 169, 229
DVU1782 iron-sulfur cluster-binding protein 169, 229
DVU1783 hypothetical protein DVU1783 169, 229
DVU1784 short chain dehydrogenase/reductase family oxidoreductase 169, 229
DVU1785 MarC membrane protein 169, 229
DVU1791 GatB/Yqey family protein 28, 94
DVU1862 GGDEF domain-containing protein 94, 229
DVU1891 hypothetical protein DVU1891 27, 169
DVU1892 glycosyl transferase group 2 family protein 94, 277
DVU2130 hypothetical protein DVU2130 5, 94
DVU2256 ruvA Holliday junction DNA helicase RuvA 94, 275
DVU2279 hypothetical protein DVU2279 94, 334
DVU2280 amino acid permease family protein 94, 334
DVU2298 glycine/betaine/L-proline ABC transporter permease 94, 235
DVU2738 methyl-accepting chemotaxis protein 94, 179
DVU2771 hypothetical protein DVU2771 27, 94
DVU3151 tRNA modifying protein 5, 94
DVU3176 UDP-glucose/GDP-mannose dehydrogenase family protein 169, 292
DVU3177 hypothetical protein DVU3177 145, 169
DVU3194 engA GTP-binding protein EngA 5, 94
DVU3204 purA adenylosuccinate synthetase 5, 94
DVU3205 transglycosylase 5, 94
DVU3327 SMR family multidrug efflux pump 94, 279
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 DVU1201
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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