Organism : Desulfovibrio vulgaris Hildenborough | Module List :
DVUA0022

ABC transporter ATP-binding protein

CircVis
Functional Annotations (4)
Function System
ABC-type antimicrobial peptide transport system, ATPase component cog/ cog
ATP binding go/ molecular_function
transport go/ biological_process
ATPase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for DVUA0022
(Mouseover regulator name to see its description)

DVUA0022 is regulated by 16 influences and regulates 0 modules.
Regulators for DVUA0022 (16)
Regulator Module Operator
DVU0230 314 tf
DVU0619
DVU0230
314 combiner
DVU0936 314 tf
DVU0936
DVU2275
314 combiner
DVU1547
DVU0230
314 combiner
DVU1572
DVU2527
314 combiner
DVU1674
DVU2532
314 combiner
DVU2251 314 tf
DVU2532 314 tf
DVUA0151 314 tf
DVU1754
DVU0436
61 combiner
DVU2527 61 tf
DVU2527
DVU0653
61 combiner
DVU2582 61 tf
DVU2832 61 tf
DVU3186
DVU2527
61 combiner

Warning: DVUA0022 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
119 2.30e+01 acCGcAcTCgTgta
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RegPredict
120 3.00e+01 ctCCtt..GcGGc.a.GgGg.Cga
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RegPredict
599 3.40e-02 tCCGcTtcgGGCacGAcCGgaT
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RegPredict
600 1.30e+00 TCggcacCgTCgaCA
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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 DVUA0022

DVUA0022 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
ABC-type antimicrobial peptide transport system, ATPase component cog/ cog
ATP binding go/ molecular_function
transport go/ biological_process
ATPase activity go/ molecular_function
Module neighborhood information for DVUA0022

DVUA0022 has total of 47 gene neighbors in modules 61, 314
Gene neighbors (47)
Gene Common Name Description Module membership
DVU0020 hypothetical protein DVU0020 99, 314
DVU0189 P4 family phage/plasmid primase 204, 314
DVU0195 hypothetical protein DVU0195 222, 314
DVU0213 hypothetical protein DVU0213 161, 314
DVU0214 tail/DNA circulation protein 58, 314
DVU0216 phage baseplate assembly protein V 58, 314
DVU0217 tail protein 58, 314
DVU0218 tail protein 37, 314
DVU0219 tail protein 58, 314
DVU0220 tail fiber protein 148, 314
DVU0221 tail fiber assembly protein 198, 314
DVU0234 hypothetical protein DVU0234 281, 314
DVU0235 hypothetical protein DVU0235 281, 314
DVU0429 ech hydrogenase subunit EchF 61, 68
DVU0431 ech hydrogenase subunit EchD 61, 68
DVU0433 ech hydrogenase subunit EchB 61, 68
DVU0434 ech hydrogenase subunit EchA 61, 68
DVU1483 tail fiber assembly protein 134, 314
DVU1484 hypothetical protein DVU1484 134, 314
DVU1486 tail fiber protein, truncation 152, 314
DVU2457 hypothetical protein DVU2457 200, 314
DVU2733 adenine specific DNA methyltransferase 82, 314
DVU2848 tail fiber assembly protein 38, 314
DVU2849 tail fiber protein 247, 314
DVU2850 tail protein 58, 314
DVU2851 tail protein 58, 314
DVU2852 tail protein 38, 314
DVU2853 phage baseplate assembly protein V 58, 314
DVU2855 tail/DNA circulation protein 314, 341
DVU2856 hypothetical protein DVU2856 38, 314
DVU3286 hypothetical protein DVU3286 61, 205
DVUA0001 hypothetical protein DVUA0001 61, 314
DVUA0002 ParA family protein 61, 68
DVUA0003 hypothetical protein DVUA0003 61, 68
DVUA0021 hypothetical protein DVUA0021 61, 192
DVUA0022 ABC transporter ATP-binding protein 61, 314
DVUA0024 sigma-54 factor interaction domain-containing protein 61, 335
DVUA0033 hypothetical protein DVUA0033 136, 314
DVUA0035 hypothetical protein DVUA0035 61, 197
DVUA0046 glycosyl transferase, group 2 family protein 3, 61
DVUA0047 hypothetical protein DVUA0047 61, 200
DVUA0064 hypothetical protein DVUA0064 61, 335
DVUA0083 hypothetical protein DVUA0083 61, 289
DVUA0092 hypothetical protein DVUA0092 61, 193
DVUA0146 hypothetical protein DVUA0146 61, 200
DVUA0148 major facilitator superfamily protein 61, 124
DVUA0149 hypothetical protein DVUA0149 61, 136
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 DVUA0022
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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