Organism : Pseudomonas aeruginosa | Module List :
PA3888

probable permease of ABC transporter (NCBI)

CircVis
Functional Annotations (5)
Function System
ABC-type proline/glycine betaine transport systems, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3888
(Mouseover regulator name to see its description)

PA3888 is regulated by 46 influences and regulates 0 modules.
Regulators for PA3888 (46)
Regulator Module Operator
PA0279 28 tf
PA0289 28 tf
PA0763 28 tf
PA1351 28 tf
PA1504 28 tf
PA2047 28 tf
PA2713 28 tf
PA2896 28 tf
PA3124 28 tf
PA4703 28 tf
PA4831 28 tf
PA4853 28 tf
PA5059 28 tf
PA5261 28 tf
PA5483 28 tf
PA5550 28 tf
PA0120 399 tf
PA0248 399 tf
PA0610 399 tf
PA0611 399 tf
PA0791 399 tf
PA0877 399 tf
PA0979 399 tf
PA1099 399 tf
PA1484 399 tf
PA1504 399 tf
PA1520 399 tf
PA1760 399 tf
PA1978 399 tf
PA2047 399 tf
PA2076 399 tf
PA2718 399 tf
PA2896 399 tf
PA2921 399 tf
PA3622 399 tf
PA3714 399 tf
PA4052 399 tf
PA4745 399 tf
PA4853 399 tf
PA4890 399 tf
PA5029 399 tf
PA5253 399 tf
PA5261 399 tf
PA5431 399 tf
PA5437 399 tf
PA5483 399 tf

Warning: PA3888 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
2892 3.20e-02 AAaATtaCggTCaTcaTataAgTt
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2893 2.00e+01 CGacCaAAAtacaaTcGcTatcG
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3622 4.00e+01 GG.atttCcctGCCgc.Cc.gAG
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3623 3.90e+02 aAac.cTcaTt.gGAa
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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 PA3888

PA3888 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
ABC-type proline/glycine betaine transport systems, permease component cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
membrane go/ cellular_component
ABC transporters kegg/ kegg pathway
Module neighborhood information for PA3888

PA3888 has total of 37 gene neighbors in modules 28, 399
Gene neighbors (37)
Gene Common Name Description Module membership
PA0231 pcaD beta-ketoadipate enol-lactone hydrolase (NCBI) 87, 399
PA0232 pcaC gamma-carboxymuconolactone decarboxylase (NCBI) 215, 399
PA0558 PA0558 hypothetical protein (NCBI) 361, 399
PA1115 PA1115 hypothetical protein (NCBI) 10, 399
PA1408 PA1408 hypothetical protein (NCBI) 28, 107
PA1562 acnA aconitate hydratase 1 (NCBI) 107, 399
PA1985 pqqA coenzyme PQQ synthesis protein PqqA (NCBI) 233, 399
PA1986 pqqB pyrroloquinoline quinone biosynthesis protein PqqB (NCBI) 233, 399
PA1987 pqqC pyrroloquinoline quinone biosynthesis protein PqqC (NCBI) 233, 399
PA1988 pqqD pyrroloquinoline quinone biosynthesis protein PqqD (NCBI) 233, 399
PA1989 pqqE pyrroloquinoline quinone biosynthesis protein PqqE (NCBI) 233, 399
PA1990 PA1990 probable peptidase (NCBI) 382, 399
PA3023 PA3023 hypothetical protein (NCBI) 28, 322
PA3026 PA3026 hypothetical protein (NCBI) 28, 489
PA3426 PA3426 enoyl-CoA hydratase (NCBI) 28, 443
PA3888 PA3888 probable permease of ABC transporter (NCBI) 28, 399
PA3889 PA3889 probable binding protein component of ABC transporter (NCBI) 28, 399
PA3890 PA3890 probable permease of ABC transporter (NCBI) 28, 399
PA3891 PA3891 probable ATP-binding component of ABC transporter (NCBI) 28, 399
PA4017 PA4017 hypothetical protein (NCBI) 2, 399
PA4345 PA4345 hypothetical protein (NCBI) 28, 322
PA4472 pmbA PmbA protein (NCBI) 28, 523
PA4474 PA4474 hypothetical protein (NCBI) 10, 28
PA4475 PA4475 hypothetical protein (NCBI) 28, 441
PA4476 PA4476 hypothetical protein (NCBI) 3, 28
PA4477 cafA cytoplasmic axial filament protein (NCBI) 28, 441
PA4478 PA4478 Maf-like protein (NCBI) 14, 28
PA4786 PA4786 short-chain dehydrogenase (NCBI) 28, 322
PA4829 lpd3 dihydrolipoamide dehydrogenase (NCBI) 28, 153
PA4830 PA4830 hypothetical protein (NCBI) 28, 101
PA4831 PA4831 probable transcriptional regulator (NCBI) 28, 101
PA4879 PA4879 hypothetical protein (NCBI) 28, 322
PA5297 poxB pyruvate dehydrogenase (cytochrome) (NCBI) 28, 483
PA5376 PA5376 probable ATP-binding component of ABC transporter (NCBI) 87, 399
PA5377 PA5377 probable permease of ABC transporter (NCBI) 87, 399
PA5473 PA5473 hypothetical protein (NCBI) 28, 328
PA5521 PA5521 probable short-chain dehydrogenase (NCBI) 28, 378
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 PA3888
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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