Organism : Pseudomonas aeruginosa | Module List :
PA2495 oprN

Multidrug efflux outer membrane protein OprN precursor (NCBI)

CircVis
Functional Annotations (6)
Function System
Outer membrane protein cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
lipid binding go/ molecular_function
membrane go/ cellular_component
outer_NodT tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA2495
(Mouseover regulator name to see its description)

PA2495 is regulated by 24 influences and regulates 0 modules.
Regulators for PA2495 oprN (24)
Regulator Module Operator
PA2259 494 tf
PA2270 494 tf
PA2276 494 tf
PA2281 494 tf
PA2320 494 tf
PA2332 494 tf
PA2337 494 tf
PA2383 494 tf
PA2387 494 tf
PA2417 494 tf
PA2423 494 tf
PA2467 494 tf
PA2468 494 tf
PA2484 494 tf
PA2492 494 tf
PA1003 108 tf
PA1484 108 tf
PA1633 108 tf
PA2320 108 tf
PA2484 108 tf
PA2488 108 tf
PA2758 108 tf
PA4070 108 tf
PA4354 108 tf

Warning: PA2495 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
3048 1.20e-28 aTagT..cTATCgAcagg..TgAT
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3049 8.80e-03 gttatc.aatCGAc.g.tcCgccc
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3802 1.40e-10 AAaAa.aC.CgTCat..tttAaaa
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3803 4.40e-06 AActT.ATgatTt...ActGc
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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 PA2495

PA2495 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Outer membrane protein cog/ cog
transporter activity go/ molecular_function
transport go/ biological_process
lipid binding go/ molecular_function
membrane go/ cellular_component
outer_NodT tigr/ tigrfam
Module neighborhood information for PA2495

PA2495 has total of 43 gene neighbors in modules 108, 494
Gene neighbors (43)
Gene Common Name Description Module membership
PA1332 PA1332 hypothetical protein (NCBI) 108, 351
PA1333 PA1333 hypothetical protein (NCBI) 108, 361
PA1743 PA1743 hypothetical protein (NCBI) 108, 446
PA1744 PA1744 hypothetical protein (NCBI) 108, 326
PA1942 PA1942 hypothetical protein (NCBI) 9, 108
PA1970 PA1970 hypothetical protein (NCBI) 108, 226
PA2018 PA2018 RND multidrug efflux transporter (NCBI) 39, 108
PA2271 PA2271 probable acetyltransferase (NCBI) 196, 494
PA2272 pbpC penicillin-binding protein 3A (NCBI) 257, 494
PA2281 PA2281 probable transcriptional regulator (NCBI) 135, 494
PA2317 PA2317 probable oxidoreductase (NCBI) 108, 291
PA2332 PA2332 probable transcriptional regulator (NCBI) 257, 494
PA2337 mtlR transcriptional regulator MtlR (NCBI) 34, 494
PA2358 PA2358 hypothetical protein (NCBI) 291, 494
PA2380 PA2380 hypothetical protein (NCBI) 257, 494
PA2383 PA2383 probable transcriptional regulator (NCBI) 257, 494
PA2387 PA2387 probable sigma-70 factor, ECF subfamily (NCBI) 257, 494
PA2388 PA2388 probable transmembrane sensor (NCBI) 257, 494
PA2417 PA2417 probable transcriptional regulator (NCBI) 257, 494
PA2423 PA2423 hypothetical protein (NCBI) 257, 494
PA2464 PA2464 hypothetical protein (NCBI) 257, 494
PA2467 PA2467 probable transmembrane sensor (NCBI) 325, 494
PA2468 PA2468 probable sigma-70 factor, ECF subfamily (NCBI) 325, 494
PA2484 PA2484 hypothetical protein (NCBI) 139, 494
PA2486 PA2486 hypothetical protein (NCBI) 441, 494
PA2491 PA2491 probable oxidoreductase (NCBI) 257, 494
PA2492 mexT transcriptional regulator MexT (NCBI) 257, 494
PA2493 mexE Resistance-Nodulation-Cell Division (RND) multidrug efflux membrane fusion protein MexE precursor (NCBI) 108, 494
PA2494 mexF Resistance-Nodulation-Cell Division (RND) multidrug efflux transporter MexF (NCBI) 108, 494
PA2495 oprN Multidrug efflux outer membrane protein OprN precursor (NCBI) 108, 494
PA2758 PA2758 probable transcriptional regulator (NCBI) 61, 108
PA2759 PA2759 hypothetical protein (NCBI) 108, 291
PA2813 PA2813 probable glutathione S-transferase (NCBI) 9, 108
PA3229 PA3229 hypothetical protein (NCBI) 108, 291
PA3230 PA3230 hypothetical protein (NCBI) 108, 109
PA4070 PA4070 probable transcriptional regulator (NCBI) 61, 108
PA4353 PA4353 hypothetical protein (NCBI) 108, 461
PA4354 PA4354 hypothetical protein (NCBI) 108, 337
PA4355 PA4355 probable major facilitator superfamily (MFS) transporter (NCBI) 101, 108
PA4356 xenB xenobiotic reductase (NCBI) 62, 108
PA4623 PA4623 hypothetical protein (NCBI) 108, 152
PA4881 PA4881 hypothetical protein (NCBI) 108, 152
PA5465 PA5465 hypothetical protein (NCBI) 70, 108
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 PA2495
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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