Organism : Pseudomonas aeruginosa | Module List :
PA0485

hypothetical protein (NCBI)

CircVis
Functional Annotations (3)
Function System
Predicted permeases cog/ cog
membrane go/ cellular_component
rarD tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0485
(Mouseover regulator name to see its description)

PA0485 is regulated by 42 influences and regulates 0 modules.
Regulators for PA0485 (42)
Regulator Module Operator
PA0037 276 tf
PA0455 276 tf
PA0763 276 tf
PA0815 276 tf
PA1226 276 tf
PA1422 276 tf
PA1627 276 tf
PA2093 276 tf
PA2196 276 tf
PA2281 276 tf
PA2484 276 tf
PA3583 276 tf
PA3622 276 tf
PA3895 276 tf
PA4057 276 tf
PA4070 276 tf
PA4120 276 tf
PA4530 276 tf
PA4745 276 tf
PA4853 276 tf
PA4890 276 tf
PA5166 276 tf
PA5239 276 tf
PA5274 276 tf
PA5356 276 tf
PA5403 276 tf
PA5438 276 tf
PA0456 261 tf
PA0791 261 tf
PA2692 261 tf
PA3002 261 tf
PA3006 261 tf
PA3622 261 tf
PA4057 261 tf
PA4275 261 tf
PA4451 261 tf
PA4530 261 tf
PA4703 261 tf
PA4745 261 tf
PA4890 261 tf
PA5337 261 tf
PA5438 261 tf

Warning: PA0485 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
3350 3.40e+03 tcATcCgC.tGCCa
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3351 2.90e+03 aAacTGcTatcAT
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3380 1.00e-01 AaAtgAAAGgtgGttAG
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3381 6.20e+00 AGGGTAGAGACGTTATTATATTA
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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 PA0485

PA0485 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Predicted permeases cog/ cog
membrane go/ cellular_component
rarD tigr/ tigrfam
Module neighborhood information for PA0485

PA0485 has total of 27 gene neighbors in modules 261, 276
Gene neighbors (27)
Gene Common Name Description Module membership
PA0148 PA0148 adenosine deaminase (NCBI) 276, 306
PA0319 PA0319 hypothetical protein (NCBI) 276, 374
PA0485 PA0485 hypothetical protein (NCBI) 261, 276
PA0542 PA0542 hypothetical protein (NCBI) 9, 261
PA0834 PA0834 hypothetical protein (NCBI) 261, 517
PA0952 PA0952 hypothetical protein (NCBI) 261, 315
PA1564 PA1564 hypothetical protein (NCBI) 41, 261
PA1727 PA1727 hypothetical protein (NCBI) 8, 261
PA2352 PA2352 probable glycerophosphoryl diester phosphodiesterase (NCBI) 276, 519
PA2584 pgsA CDP-diacylglycerol--glycerol-3-phosphate 3-phosphatidyltransferase (NCBI) 117, 261
PA2666 PA2666 probable 6-pyruvoyl tetrahydrobiopterin synthase (NCBI) 99, 261
PA2973 PA2973 probable peptidase (NCBI) 18, 261
PA2974 PA2974 probable hydrolase (NCBI) 261, 296
PA2975 rluC ribosomal large subunit pseudouridine synthase C (NCBI) 261, 296
PA3431 PA3431 hypothetical protein (NCBI) 224, 261
PA3432 PA3432 hypothetical protein (NCBI) 224, 261
PA3537 argF ornithine carbamoyltransferase, anabolic (NCBI) 276, 490
PA5066 hisI phosphoribosyl-AMP cyclohydrolase (NCBI) 8, 261
PA5260 hemC porphobilinogen deaminase (NCBI) 261, 296
PA5443 uvrD DNA helicase II (NCBI) 117, 261
PA5462 PA5462 hypothetical protein (NCBI) 276, 286
PA5463 PA5463 hypothetical protein (NCBI) 276, 544
PA5498 PA5498 probable adhesin (NCBI) 18, 276
PA5499 np20 transcriptional regulator np20 (NCBI) 18, 276
PA5500 znuC zinc transport protein ZnuC (NCBI) 18, 276
PA5501 znuB permease of ABC zinc transporter ZnuB (NCBI) 18, 276
PA5502 PA5502 hypothetical protein (NCBI) 18, 276
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 PA0485
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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