Organism : Pseudomonas aeruginosa | Module List :
PA3641

probable amino acid permease (NCBI)

CircVis
Functional Annotations (5)
Function System
Na+/alanine symporter cog/ cog
sodium:amino acid symporter activity go/ molecular_function
sodium ion transport go/ biological_process
membrane go/ cellular_component
agcS tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3641
(Mouseover regulator name to see its description)

PA3641 is regulated by 57 influences and regulates 0 modules.
Regulators for PA3641 (57)
Regulator Module Operator
PA0376 314 tf
PA0455 314 tf
PA0780 314 tf
PA0815 314 tf
PA0890 314 tf
PA0961 314 tf
PA1125 314 tf
PA2047 314 tf
PA2622 314 tf
PA2899 314 tf
PA3002 314 tf
PA3126 314 tf
PA3458 314 tf
PA3622 314 tf
PA3776 314 tf
PA3921 314 tf
PA4021 314 tf
PA4052 314 tf
PA4094 314 tf
PA4279 314 tf
PA4853 314 tf
PA4890 314 tf
PA5157 314 tf
PA5403 314 tf
PA5550 314 tf
PA5562 314 tf
PA0155 269 tf
PA0179 269 tf
PA0376 269 tf
PA0479 269 tf
PA0512 269 tf
PA0780 269 tf
PA0815 269 tf
PA0893 269 tf
PA0961 269 tf
PA1125 269 tf
PA2047 269 tf
PA2547 269 tf
PA2622 269 tf
PA2899 269 tf
PA3002 269 tf
PA3126 269 tf
PA3458 269 tf
PA3622 269 tf
PA3776 269 tf
PA3778 269 tf
PA4021 269 tf
PA4052 269 tf
PA4094 269 tf
PA4279 269 tf
PA4853 269 tf
PA4890 269 tf
PA5157 269 tf
PA5337 269 tf
PA5403 269 tf
PA5550 269 tf
PA5562 269 tf

Warning: PA3641 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
3366 1.60e+01 AagcatcgCGCcCtttct.gact
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3367 4.00e+02 GgAAAggtgtT
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3454 4.90e+00 tAtAATgCgcCaCttTtttctCcg
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3455 2.30e+01 GgAAAggt.tT
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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 PA3641

PA3641 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Na+/alanine symporter cog/ cog
sodium:amino acid symporter activity go/ molecular_function
sodium ion transport go/ biological_process
membrane go/ cellular_component
agcS tigr/ tigrfam
Module neighborhood information for PA3641

PA3641 has total of 18 gene neighbors in modules 269, 314
Gene neighbors (18)
Gene Common Name Description Module membership
PA0165 PA0165 hypothetical protein (NCBI) 269, 314
PA0382 micA tRNA (guanine-N(7)-)-methyltransferase (NCBI) 269, 360
PA0916 PA0916 hypothetical protein (NCBI) 269, 314
PA1228 PA1228 hypothetical protein (NCBI) 269, 314
PA1687 speE spermidine synthase (NCBI) 314, 520
PA3607 potA polyamine transport protein PotA (NCBI) 230, 314
PA3608 potB polyamine transport protein PotB (NCBI) 269, 314
PA3609 potC polyamine transport protein PotC (NCBI) 269, 314
PA3610 potD polyamine transport protein PotD (NCBI) 269, 314
PA3641 PA3641 probable amino acid permease (NCBI) 269, 314
PA3713 PA3713 hypothetical protein (NCBI) 269, 314
PA3823 tgt queuine tRNA-ribosyltransferase (NCBI) 269, 314
PA4645 PA4645 hypoxanthine-guanine phosphoribosyltransferase (NCBI) 269, 314
PA4719 PA4719 probable transporter (NCBI) 269, 314
PA4720 trmA tRNA (uracil-5-)-methyltransferase (NCBI) 269, 314
PA5117 typA regulatory protein TypA (NCBI) 90, 269
PA5336 gmk guanylate kinase (NCBI) 90, 269
PA5479 gltP proton-glutamate symporter (NCBI) 269, 272
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 PA3641
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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