Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVU1057

cobalt ABC transporter permease

CircVis
Functional Annotations (6)
Function System
ABC-type cobalt transport system, permease component CbiQ and related transporters cog/ cog
cobalt ion transport go/ biological_process
cobalamin biosynthetic process go/ biological_process
cobalt ion transmembrane transporter activity go/ molecular_function
ABC transporters kegg/ kegg pathway
CbiQ_TIGR tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVU1057
(Mouseover regulator name to see its description)

DVU1057 is regulated by 16 influences and regulates 0 modules.
Regulators for DVU1057 (16)
Regulator Module Operator
DVU0539
DVU1419
309 combiner
DVU1744 309 tf
DVU2567
DVU3334
309 combiner
DVU3080 309 tf
DVU3255
DVU1744
309 combiner
DVU3334
DVU0230
309 combiner
DVUA0143 309 tf
DVU0110 145 tf
DVU0230 145 tf
DVU0653
DVU1063
145 combiner
DVU0653
DVU1690
145 combiner
DVU1517 145 tf
DVU1518
DVU2086
145 combiner
DVU1628 145 tf
DVU1754
DVU3381
145 combiner
DVU2532
DVU0653
145 combiner

Warning: DVU1057 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
277 3.80e-01 atttctTgaTTgatcAaACagttt
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RegPredict
278 1.90e+02 cCcTgAccAcGcAac
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RegPredict
591 1.50e-03 Acgattcaa.gcgcaA.aaCAcAg
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RegPredict
592 8.20e-01 t.aTAgt.tTctcaaAaActa
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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 DVU1057

DVU1057 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
ABC-type cobalt transport system, permease component CbiQ and related transporters cog/ cog
cobalt ion transport go/ biological_process
cobalamin biosynthetic process go/ biological_process
cobalt ion transmembrane transporter activity go/ molecular_function
ABC transporters kegg/ kegg pathway
CbiQ_TIGR tigr/ tigrfam
Module neighborhood information for DVU1057

DVU1057 has total of 49 gene neighbors in modules 145, 309
Gene neighbors (49)
Gene Common Name Description Module membership
DVU0012 hypothetical protein DVU0012 206, 309
DVU0041 Slt family transglycosylase 145, 146
DVU0092 sensory box histidine kinase 145, 348
DVU0408 response regulator/sensory box/GGDEF domain/EAL domain-containing protein 121, 309
DVU0438 AcrB/AcrD/AcrF family protein 166, 309
DVU0528 phosphatidylglycerophosphatase 309, 330
DVU0537 hypothetical protein DVU0537 225, 309
DVU0616 hypothetical protein DVU0616 46, 309
DVU0666 HD domain-containing protein 214, 309
DVU0674 His/Glu/Gln/Arg/opine ABC transporter permease 309, 332
DVU0852 extracellular solute-binding protein 127, 309
DVU0876 metallo-beta-lactamase family protein 145, 172
DVU0952 hypothetical protein DVU0952 52, 145
DVU1057 cobalt ABC transporter permease 145, 309
DVU1058 cbiM cobalt transport protein CbiM 6, 145
DVU1354 hypothetical protein DVU1354 215, 309
DVU1425 gcvPA glycine dehydrogenase subunit 1 14, 309
DVU1460 hypothetical protein DVU1460 145, 334
DVU1473 hypothetical protein DVU1473 155, 309
DVU1632 PTS system transporter subunit IIA 309, 330
DVU1937 phosphonate ABC transporter periplasmic phosphonate-binding protein 145, 262
DVU1989 hypothetical protein DVU1989 214, 309
DVU2083 relA GTP pyrophosphokinase 145, 318
DVU2261 hypothetical protein DVU2261 57, 309
DVU2285 L-lactate permease family protein 145, 306
DVU2286 hydrogenase subunit CooM 145, 207
DVU2287 hydrogenase subunit CooK 145, 346
DVU2289 hydrogenase subunit CooX 145, 207
DVU2291 carbon monoxide-induced hydrogenase CooH 145, 207
DVU2328 hydrogenase nickel insertion protein HypA 145, 249
DVU2580 response regulator 145, 251
DVU2619 hypothetical protein DVU2619 145, 162
DVU2745 hypothetical protein DVU2745 263, 309
DVU2746 hypothetical protein DVU2746 225, 309
DVU2845 HIT family protein 90, 309
DVU2944 ErfK/YbiS/YcfS/YnhG family protein 55, 145
DVU2945 hypothetical protein DVU2945 145, 278
DVU2980 pssA CDP-diacylglycerol--serine O-phosphatidyltransferase 145, 308
DVU3005 aminotransferase 22, 145
DVU3144 cytochrome c family protein 309, 321
DVU3145 hydrogenase, b-type cytochrome subunit 214, 309
DVU3157 hypothetical protein DVU3157 145, 250
DVU3158 vacJ lipoprotein 26, 145
DVU3177 hypothetical protein DVU3177 145, 169
DVU3190 hypothetical protein DVU3190 145, 176
DVU3221 sensor histidine kinase 115, 145
DVU3273 hypothetical protein DVU3273 145, 186
DVU3380 hypothetical protein DVU3380 309, 330
DVUA0138 sensor histidine kinase 145, 185
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 DVU1057
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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