Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1047 ccmC

cytochrome c-type biogenesis protein CcmC

CircVis
Functional Annotations (7)
Function System
ABC-type transport system involved in cytochrome c biogenesis, permease component cog/ cog
respiratory chain complex IV assembly go/ biological_process
heme transporter activity go/ molecular_function
heme transport go/ biological_process
membrane go/ cellular_component
cytochrome complex assembly go/ biological_process
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1047
(Mouseover regulator name to see its description)

DVU1047 is regulated by 19 influences and regulates 0 modules.
Regulators for DVU1047 ccmC (19)
Regulator Module Operator
DVU0682
DVU3255
251 combiner
DVU1518
DVU2086
251 combiner
DVU1561 251 tf
DVU2086
DVU1547
251 combiner
DVU2086
DVU3142
251 combiner
DVU2423
DVU2832
251 combiner
DVU2582 251 tf
DVU3167
DVU2582
251 combiner
DVU3255
DVU0110
251 combiner
DVU0619
DVU0230
52 combiner
DVU0653
DVU2582
52 combiner
DVU0744
DVU0230
52 combiner
DVU0744
DVU3142
52 combiner
DVU1561
DVUA0024
52 combiner
DVU3167
DVU1690
52 combiner
DVU3167
DVU2582
52 combiner
DVU3255
DVU1690
52 combiner
DVU3255
DVU2251
52 combiner
DVU3255
DVU2275
52 combiner

Warning: DVU1047 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
101 1.10e+01 cTtcagGAggA
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RegPredict
102 8.10e+00 GtTtTTCt
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RegPredict
479 4.30e+02 CAatTttccGcaA.A
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RegPredict
480 1.70e+04 A.ATcCTGCTcGAA
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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 DVU1047

DVU1047 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
ABC-type transport system involved in cytochrome c biogenesis, permease component cog/ cog
respiratory chain complex IV assembly go/ biological_process
heme transporter activity go/ molecular_function
heme transport go/ biological_process
membrane go/ cellular_component
cytochrome complex assembly go/ biological_process
ABC transporters kegg/ kegg pathway
Module neighborhood information for DVU1047

DVU1047 has total of 40 gene neighbors in modules 52, 251
Gene neighbors (40)
Gene Common Name Description Module membership
DVU0075 aminotransferase 95, 251
DVU0076 glycosyl transferase group 2 family protein 14, 251
DVU0293 dksA/traR C4-type zinc finger family protein 251, 331
DVU0341 3-deoxy-manno-octulosonate cytidylyltransferase 251, 292
DVU0397 rare lipoprotein A 52, 55
DVU0642 alpha/beta fold family hydrolase 52, 221
DVU0842 hypothetical protein DVU0842 52, 137
DVU0952 hypothetical protein DVU0952 52, 145
DVU1001 coenzyme A binding protein 52, 172
DVU1045 hypothetical protein DVU1045 52, 251
DVU1047 ccmC cytochrome c-type biogenesis protein CcmC 52, 251
DVU1048 ccmB cytochrome c-type biogenesis protein CcmB 12, 251
DVU1049 ABC transporter ATP-binding protein 251, 306
DVU1050 ccmF cytochrome c-type biogenesis protein CcmF 52, 300
DVU1070 branched chain amino acid ABC transporter ATP-binding protein 221, 251
DVU1094 argH argininosuccinate lyase 220, 251
DVU1282 glmM phosphoglucosamine mutase 52, 188
DVU1286 reductase, transmembrane subunit 52, 251
DVU1658 translaldolase 6, 251
DVU1842 lipoprotein 186, 251
DVU1864 DNA-binding protein HU subunit beta 52, 297
DVU1865 hypothetical protein DVU1865 52, 128
DVU1907 ugd UDP-glucose 6-dehydrogenase 65, 251
DVU1911 CBS domain-containing protein 251, 292
DVU1919 hydrogenase expression/formation protein 52, 154
DVU1928 lspA lipoprotein signal peptidase 52, 75
DVU2368 fabZ (3R)-hydroxymyristoyl-ACP dehydratase 52, 174
DVU2369 lpxD UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase 174, 251
DVU2580 response regulator 145, 251
DVU2886 AraC family transcriptional regulator 251, 304
DVU2887 hypothetical protein DVU2887 106, 251
DVU2943 pyrE orotate phosphoribosyltransferase 52, 55
DVU3055 ribonuclease 221, 251
DVU3056 hypothetical protein DVU3056 78, 251
DVU3163 ABC transporter permease 174, 251
DVU3191 rluC ribosomal large subunit pseudouridine synthase C 52, 308
DVU3210 thrC threonine synthase 52, 344
DVU3229 fliA RNA polymerase sigma factor for flagellar operon FliA 251, 304
DVU3272 hypothetical protein 178, 251
DVU3281 hypothetical protein DVU3281 52, 63
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 DVU1047
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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