Organism : Pseudomonas aeruginosa | Module List :
PA1099 fleR

two-component response regulator (NCBI)

CircVis
Functional Annotations (9)
Function System
Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-binding domains cog/ cog
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
sequence-specific DNA binding transcription factor activity go/ molecular_function
ATP binding go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
transcription factor binding go/ molecular_function
nucleoside-triphosphatase activity go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA1099
(Mouseover regulator name to see its description)

PA1099 is regulated by 29 influences and regulates 37 modules.
Regulators for PA1099 fleR (29)
Regulator Module Operator
PA0120 437 tf
PA0121 437 tf
PA0179 437 tf
PA0424 437 tf
PA0491 437 tf
PA1097 437 tf
PA1099 437 tf
PA1229 437 tf
PA1269 437 tf
PA1430 437 tf
PA1455 437 tf
PA1607 437 tf
PA1633 437 tf
PA1978 437 tf
PA2511 437 tf
PA2586 437 tf
PA2588 437 tf
PA3398 437 tf
PA3973 437 tf
PA5380 437 tf
PA5483 437 tf
PA0179 530 tf
PA1099 530 tf
PA1430 530 tf
PA1455 530 tf
PA2586 530 tf
PA3815 530 tf
PA5380 530 tf
PA5438 530 tf

Warning: PA1099 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
3694 1.10e-12 g.gAat.ATGGCtataTgccATta
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3695 1.40e-01 AaGAAACgggcAtCaa.agTtTta
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3874 2.80e-02 tTGcAacgG.ttaaGCAAtgg
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3875 8.80e-01 aACgacatttaaTcgAcgAAT
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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 PA1099

PA1099 is enriched for 9 functions in 3 categories.
Module neighborhood information for PA1099

PA1099 has total of 32 gene neighbors in modules 437, 530
Gene neighbors (32)
Gene Common Name Description Module membership
PA1097 fleQ transcriptional regulator FleQ (NCBI) 437, 551
PA1098 fleS two-component sensor (NCBI) 275, 530
PA1099 fleR two-component response regulator (NCBI) 437, 530
PA1100 fliE flagellar hook-basal body complex protein (NCBI) 275, 530
PA1101 fliF flagellar M-ring protein (NCBI) 275, 530
PA1102 fliG flagellar motor protein (NCBI) 242, 530
PA1452 flhA flagellar biosynthesis protein (NCBI) 275, 530
PA1453 flhF flagellar biosynthesis protein (NCBI) 275, 530
PA1454 fleN flagellar synthesis regulator FleN (NCBI) 242, 530
PA1455 fliA flagellar biosynthesis sigma factor FliA (NCBI) 242, 530
PA1458 PA1458 probable two-component sensor (NCBI) 242, 530
PA1463 PA1463 hypothetical protein (NCBI) 437, 530
PA1464 PA1464 probable purine-binding chemotaxis protein (NCBI) 242, 530
PA1474 PA1474 hypothetical protein (NCBI) 437, 496
PA1545 PA1545 hypothetical protein (NCBI) 437, 496
PA2652 PA2652 probable chemotaxis transducer (NCBI) 437, 496
PA2654 PA2654 probable chemotaxis transducer (NCBI) 437, 496
PA2867 PA2867 probable chemotaxis transducer (NCBI) 437, 496
PA3340 PA3340 hypothetical protein (NCBI) 388, 437
PA3348 PA3348 probable chemotaxis protein methyltransferase (NCBI) 437, 496
PA3349 PA3349 probable chemotaxis protein (NCBI) 437, 530
PA3350 PA3350 flagellar basal body P-ring biosynthesis protein (NCBI) 437, 530
PA3351 PA3351 hypothetical protein (NCBI) 437, 530
PA3352 PA3352 hypothetical protein (NCBI) 437, 530
PA3353 PA3353 hypothetical protein (NCBI) 437, 496
PA3526 PA3526 probable outer membrane protein precursor (NCBI) 437, 496
PA3662 PA3662 hypothetical protein (NCBI) 437, 496
PA4309 pctA chemotactic transducer PctA (NCBI) 437, 496
PA4310 pctB chemotactic transducer PctB (NCBI) 437, 496
PA4324 PA4324 hypothetical protein (NCBI) 437, 455
PA4633 PA4633 probable chemotaxis transducer (NCBI) 437, 496
PA4843 PA4843 probable two-component response regulator (NCBI) 437, 496
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 PA1099
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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