Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU3057

oxygen-independent coproporphyrinogen III oxidase

CircVis
Functional Annotations (10)
Function System
Coproporphyrinogen III oxidase and related Fe-S oxidoreductases cog/ cog
coproporphyrinogen oxidase activity go/ molecular_function
cytoplasm go/ cellular_component
porphyrin-containing compound biosynthetic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
coproporphyrinogen dehydrogenase activity go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
hemN_rel tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU3057
(Mouseover regulator name to see its description)

DVU3057 is regulated by 18 influences and regulates 0 modules.
Regulators for DVU3057 (18)
Regulator Module Operator
DVU0653 284 tf
DVU0653
DVU1744
284 combiner
DVU1517 284 tf
DVU2633
DVU1744
284 combiner
DVU2690 284 tf
DVU2886
DVU1754
284 combiner
DVUA0024 284 tf
DVUA0057 284 tf
DVUA0143 284 tf
DVU0309
DVU2832
82 combiner
DVU0621
DVU2690
82 combiner
DVU0679
DVU2690
82 combiner
DVU1754
DVU2802
82 combiner
DVU1754
DVU3305
82 combiner
DVU2423
DVU0621
82 combiner
DVU2557
DVU3080
82 combiner
DVU2686 82 tf
DVUA0151 82 tf

Warning: DVU3057 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
161 1.40e+01 a.acaacgacc.acgCAA.Gaaac
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RegPredict
162 1.70e+04 GCgGAAGGCccgCtgGCGcC
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RegPredict
543 7.00e+01 gC.CacCATCc
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RegPredict
544 5.00e+02 gCCttCGgCAacGtc
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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 DVU3057

DVU3057 is enriched for 10 functions in 3 categories.
Enrichment Table (10)
Function System
Coproporphyrinogen III oxidase and related Fe-S oxidoreductases cog/ cog
coproporphyrinogen oxidase activity go/ molecular_function
cytoplasm go/ cellular_component
porphyrin-containing compound biosynthetic process go/ biological_process
iron-sulfur cluster binding go/ molecular_function
coproporphyrinogen dehydrogenase activity go/ molecular_function
Porphyrin and chlorophyll metabolism kegg/ kegg pathway
Metabolic pathways kegg/ kegg pathway
Biosynthesis of secondary metabolites kegg/ kegg pathway
hemN_rel tigr/ tigrfam
Module neighborhood information for DVU3057

DVU3057 has total of 45 gene neighbors in modules 82, 284
Gene neighbors (45)
Gene Common Name Description Module membership
DVU0008 hypothetical protein DVU0008 39, 284
DVU0066 cytidine/deoxycytidylate deaminase domain-containing protein 44, 82
DVU0099 TonB domain-containing protein 82, 256
DVU0117 glycosyl transferase group 2 family protein 15, 82
DVU0119 sensor histidine kinase 82, 112
DVU0120 ABC transporter substrate-binding protein 82, 112
DVU0171 hemolysin-like protein 82, 238
DVU0181 modB molybdenum ABC transporter permease 284, 329
DVU0185 hypothetical protein DVU0185 284, 299
DVU0283 AhpF family protein/thioredoxin reductase 284, 329
DVU0440 hypothetical protein DVU0440 82, 315
DVU0496 polA DNA polymerase I 25, 82
DVU0643 thiF protein 82, 84
DVU0687 tungsten-containing aldehyde:ferredoxin oxidoreductase 82, 304
DVU0689 rnhA ribonuclease H 82, 304
DVU0826 glycolate oxidase, iron-sulfur subunit 82, 291
DVU0829 ptsI phosphoenolpyruvate-protein phosphotransferase 82, 291
DVU0858 lipoprotein 82, 184
DVU0877 hypothetical protein DVU0877 160, 284
DVU1079 trmE tRNA modification GTPase TrmE 31, 82
DVU1261 hypothetical protein DVU1261 82, 260
DVU1268 hypothetical protein DVU1268 82, 172
DVU1416 hypothetical protein DVU1416 284, 329
DVU1573 pth peptidyl-tRNA hydrolase 82, 278
DVU1899 DNA repair protein RecO 25, 284
DVU2115 hypothetical protein DVU2115 82, 267
DVU2147 L-serine dehydratase 68, 284
DVU2204 tnaA tryptophanase 133, 284
DVU2303 hypothetical protein DVU2303 51, 284
DVU2334 hypothetical protein DVU2334 284, 329
DVU2346 hypothetical protein DVU2346 284, 329
DVU2591 tail fiber assembly protein 82, 106
DVU2661 twin-arginine translocation pathway signal sequence domain-containing protein 15, 82
DVU2733 adenine specific DNA methyltransferase 82, 314
DVU2822 TRAP transporter solute receptor DctP 82, 211
DVU2824 formate acetyltransferase 82, 211
DVU3000 hypothetical protein DVU3000 15, 284
DVU3007 hypothetical protein DVU3007 15, 284
DVU3034 hypothetical protein DVU3034 36, 284
DVU3057 oxygen-independent coproporphyrinogen III oxidase 82, 284
DVU3058 sensory box histidine kinase/response regulator 82, 202
DVU3214 phosphoenolpyruvate synthase-like protein 67, 284
DVU3236 hflX GTP-binding protein HflX 51, 82
DVU3258 murA UDP-N-acetylglucosamine 1-carboxyvinyltransferase 82, 270
DVU3326 SMR family multidrug efflux pump 82, 256
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 DVU3057
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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