Organism : Pseudomonas aeruginosa | Module List :
PA0527 dnr

transcriptional regulator Dnr (NCBI)

CircVis
Functional Annotations (4)
Function System
cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0527
(Mouseover regulator name to see its description)

PA0527 is regulated by 29 influences and regulates 22 modules.
Regulators for PA0527 dnr (29)
Regulator Module Operator
PA0448 162 tf
PA0515 162 tf
PA0527 162 tf
PA1050 162 tf
PA1196 162 tf
PA2126 162 tf
PA2622 162 tf
PA3458 162 tf
PA3879 162 tf
PA3973 162 tf
PA4853 162 tf
PA5550 162 tf
PA0279 225 tf
PA0393 225 tf
PA0416 225 tf
PA0515 225 tf
PA0527 225 tf
PA0652 225 tf
PA0707 225 tf
PA2020 225 tf
PA2126 225 tf
PA2885 225 tf
PA3458 225 tf
PA3879 225 tf
PA4094 225 tf
PA4269 225 tf
PA4493 225 tf
PA4890 225 tf
PA5105 225 tf

Warning: PA0527 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
3152 2.90e-10 tTGAtcCaggtCAa
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3153 2.70e-01 TTaa..aAg.aTTaa
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3278 7.20e-09 TTGacgCagatCAgg
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3279 2.50e+04 TGTaATAGTT
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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 PA0527

PA0527 is enriched for 4 functions in 3 categories.
Module neighborhood information for PA0527

PA0527 has total of 39 gene neighbors in modules 162, 225
Gene neighbors (39)
Gene Common Name Description Module membership
PA0200 PA0200 hypothetical protein (NCBI) 162, 429
PA0295 PA0295 probable periplasmic polyamine binding protein (NCBI) 225, 364
PA0359 PA0359 hypothetical protein (NCBI) 225, 452
PA0401 pyrC dihydroorotase (NCBI) 47, 225
PA0402 pyrB aspartate carbamoyltransferase catalytic subunit (NCBI) 47, 225
PA0527 dnr transcriptional regulator Dnr (NCBI) 162, 225
PA0545 PA0545 hypothetical protein (NCBI) 162, 375
PA1049 pdxH pyridoxamine 5'-phosphate oxidase (NCBI) 162, 225
PA1050 PA1050 hypothetical protein (NCBI) 162, 253
PA1076 PA1076 hypothetical protein (NCBI) 162, 416
PA1196 PA1196 probable transcriptional regulator (NCBI) 68, 162
PA1197 PA1197 NAD-dependent deacetylase (NCBI) 68, 162
PA1414 PA1414 hypothetical protein (NCBI) 162, 416
PA1429 PA1429 probable cation-transporting P-type ATPase (NCBI) 21, 162
PA2126 PA2126 hypothetical protein (NCBI) 162, 321
PA2127 PA2127 hypothetical protein (NCBI) 162, 225
PA2630 PA2630 hypothetical protein (NCBI) 225, 270
PA3054 PA3054 hypothetical protein (NCBI) 162, 225
PA3458 PA3458 probable transcriptional regulator (NCBI) 38, 162
PA3566 PA3566 hypothetical protein (NCBI) 225, 278
PA3567 PA3567 probable oxidoreductase (NCBI) 225, 278
PA3572 PA3572 hypothetical protein (NCBI) 162, 416
PA3631 PA3631 hypothetical protein (NCBI) 225, 312
PA3839 PA3839 probable sodium:sulfate symporter (NCBI) 162, 225
PA3859 PA3859 carboxylesterase (NCBI) 220, 225
PA3878 narX two-component sensor NarX (NCBI) 162, 225
PA3879 narL two-component response regulator NarL (NCBI) 38, 162
PA4235 bfrA bacterioferritin (NCBI) 162, 225
PA4357 PA4357 hypothetical protein (NCBI) 162, 553
PA4358 PA4358 probable ferrous iron transport protein (NCBI) 162, 553
PA4359 PA4359 hypothetical protein (NCBI) 162, 553
PA4571 PA4571 probable cytochrome c (NCBI) 38, 225
PA4610 PA4610 hypothetical protein (NCBI) 38, 162
PA5051 argS arginyl-tRNA synthetase (NCBI) 225, 452
PA5052 PA5052 hypothetical protein (NCBI) 225, 270
PA5110 fbp fructose-1,6-bisphosphatase (NCBI) 59, 225
PA5230 PA5230 probable permease of ABC transporter (NCBI) 38, 225
PA5231 PA5231 probable ATP-binding/permease fusion ABC transporter (NCBI) 38, 225
PA5494 PA5494 hypothetical protein (NCBI) 225, 452
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 PA0527
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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