Organism : Pseudomonas aeruginosa | Module List :
PA0652 vfr

transcriptional regulator Vfr (NCBI)

CircVis
Functional Annotations (5)
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
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0652
(Mouseover regulator name to see its description)

PA0652 is regulated by 33 influences and regulates 48 modules.
Regulators for PA0652 vfr (33)
Regulator Module Operator
PA0034 364 tf
PA0416 364 tf
PA0514 364 tf
PA0652 364 tf
PA0961 364 tf
PA1003 364 tf
PA1050 364 tf
PA1097 364 tf
PA1713 364 tf
PA3002 364 tf
PA3574 364 tf
PA3845 364 tf
PA3879 364 tf
PA4269 364 tf
PA4530 364 tf
PA4547 364 tf
PA5125 364 tf
PA5403 364 tf
PA0652 237 tf
PA0765 237 tf
PA1539 237 tf
PA2376 237 tf
PA3249 237 tf
PA3965 237 tf
PA4057 237 tf
PA4269 237 tf
PA4270 237 tf
PA4462 237 tf
PA4745 237 tf
PA4755 237 tf
PA5253 237 tf
PA5308 237 tf
PA5344 237 tf

Warning: PA0652 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
3302 3.40e+00 att.Ctg.cagAct.C.cGatt
Loader icon
3303 2.60e+02 AgAaaCaAGAA
Loader icon
3552 2.40e+01 AGAgAA.AaagaA.A
Loader icon
3553 4.70e+01 TTcCTGttC
Loader icon
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 PA0652

PA0652 is enriched for 5 functions in 3 categories.
Module neighborhood information for PA0652

PA0652 has total of 37 gene neighbors in modules 237, 364
Gene neighbors (37)
Gene Common Name Description Module membership
PA0020 PA0020 hypothetical protein (NCBI) 120, 364
PA0055 PA0055 hypothetical protein (NCBI) 237, 513
PA0291 oprE Anaerobically-induced outer membrane porin OprE precursor (NCBI) 120, 364
PA0295 PA0295 probable periplasmic polyamine binding protein (NCBI) 225, 364
PA0396 pilU twitching motility protein PilU (NCBI) 120, 364
PA0408 pilG twitching motility protein PilG (NCBI) 120, 364
PA0409 pilH twitching motility protein PilH (NCBI) 120, 364
PA0410 pilI twitching motility protein PilI (NCBI) 120, 364
PA0411 pilJ twitching motility protein PilJ (NCBI) 120, 364
PA0412 pilK methyltransferase PilK (NCBI) 120, 364
PA0413 chpA putative chemotactic signal transduction system (NCBI) 120, 364
PA0414 chpB probable methylesterase (NCBI) 120, 364
PA0415 chpC probable chemotaxis protein (NCBI) 120, 364
PA0555 fda fructose-bisphosphate aldolase (NCBI) 237, 273
PA0652 vfr transcriptional regulator Vfr (NCBI) 237, 364
PA0943 PA0943 hypothetical protein (NCBI) 237, 273
PA1493 cysP sulfate-binding protein of ABC transporter (NCBI) 222, 237
PA1805 ppiD peptidyl-prolyl cis-trans isomerase D (NCBI) 223, 237
PA2760 PA2760 probable outer membrane protein precursor (NCBI) 234, 237
PA3114 truA tRNA-pseudouridine synthase I (NCBI) 120, 364
PA3115 fimV Motility protein FimV (NCBI) 120, 364
PA3440 PA3440 hypothetical protein (NCBI) 237, 435
PA3861 rhl ATP-dependent RNA helicase RhlB (RefSeq) 237, 312
PA4329 pykA pyruvate kinase (NCBI) 237, 381
PA4441 PA4441 hypothetical protein (NCBI) 237, 273
PA4528 pilD type 4 prepilin peptidase PilD (NCBI) 120, 364
PA4529 coaE dephospho-CoA kinase (NCBI) 82, 364
PA4847 accB biotin carboxyl carrier protein (BCCP) (NCBI) 237, 256
PA4848 accC biotin carboxylase (NCBI) 237, 256
PA4941 hflC protease subunit HflC (NCBI) 182, 237
PA5039 aroK shikimate kinase (NCBI) 120, 364
PA5040 pilQ Type 4 fimbrial biogenesis outer membrane protein PilQ precursor (NCBI) 120, 364
PA5041 pilP type 4 fimbrial biogenesis protein PilP (NCBI) 120, 364
PA5042 pilO type 4 fimbrial biogenesis protein PilO (NCBI) 120, 364
PA5043 pilN type 4 fimbrial biogenesis protein PilN (NCBI) 120, 364
PA5044 pilM type 4 fimbrial biogenesis protein PilM (NCBI) 120, 364
PA5078 PA5078 hypothetical protein (NCBI) 237, 273
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 PA0652
Please add your comments for this gene by using the form below. Your comments will be publicly available.

comments powered by Disqus

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