Organism : Pseudomonas aeruginosa | Module List :
PA4856 retS

regulator of exopolysaccharide and type III secretion (NCBI)

CircVis
Functional Annotations (8)
Function System
Signal transduction histidine kinase cog/ cog
two-component sensor activity go/ molecular_function
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4856
(Mouseover regulator name to see its description)

PA4856 is regulated by 47 influences and regulates 0 modules.
Regulators for PA4856 retS (47)
Regulator Module Operator
PA0456 59 tf
PA0576 59 tf
PA0893 59 tf
PA1269 59 tf
PA1504 59 tf
PA3804 59 tf
PA4052 59 tf
PA4269 59 tf
PA4270 59 tf
PA4275 59 tf
PA4279 59 tf
PA4451 59 tf
PA4462 59 tf
PA4745 59 tf
PA4769 59 tf
PA4853 59 tf
PA4890 59 tf
PA5337 59 tf
PA5344 59 tf
PA0393 552 tf
PA0611 552 tf
PA0765 552 tf
PA0893 552 tf
PA0905 552 tf
PA1526 552 tf
PA2586 552 tf
PA2622 552 tf
PA2849 552 tf
PA3002 552 tf
PA3067 552 tf
PA3124 552 tf
PA3565 552 tf
PA3583 552 tf
PA3804 552 tf
PA4070 552 tf
PA4074 552 tf
PA4185 552 tf
PA4238 552 tf
PA4269 552 tf
PA4462 552 tf
PA4755 552 tf
PA4787 552 tf
PA5166 552 tf
PA5239 552 tf
PA5301 552 tf
PA5550 552 tf
PA5562 552 tf

Warning: PA4856 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
2950 9.10e+02 GccgCGCTtGC
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2951 3.90e+03 cgCGGgtt..TtC.tcTCtct
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3916 1.60e-05 CcCgttAtAatCccgcatTt
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3917 2.90e+00 AaAACGGatGgGTAtCctAGCAT
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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 PA4856

PA4856 is enriched for 8 functions in 3 categories.
Enrichment Table (8)
Function System
Signal transduction histidine kinase cog/ cog
two-component sensor activity go/ molecular_function
two-component response regulator activity go/ molecular_function
two-component signal transduction system (phosphorelay) go/ biological_process
ATP binding go/ molecular_function
regulation of transcription, DNA-dependent go/ biological_process
membrane go/ cellular_component
peptidyl-histidine phosphorylation go/ biological_process
Module neighborhood information for PA4856

PA4856 has total of 33 gene neighbors in modules 59, 552
Gene neighbors (33)
Gene Common Name Description Module membership
PA0369 PA0369 hypothetical protein (NCBI) 37, 552
PA0371 PA0371 hypothetical protein (NCBI) 37, 552
PA0372 PA0372 probable zinc protease (NCBI) 341, 552
PA0373 ftsY signal recognition particle receptor FtsY (NCBI) 424, 552
PA0374 ftsE cell division protein FtsE (NCBI) 18, 552
PA0554 PA0554 hypothetical protein (NCBI) 59, 195
PA0705 PA0705 probable glycosyl transferase (NCBI) 59, 263
PA0832 PA0832 hypothetical protein (NCBI) 31, 59
PA0965 ruvC Holliday junction resolvase (NCBI) 59, 69
PA1162 dapE succinyl-diaminopimelate desuccinylase (NCBI) 59, 281
PA1193 PA1193 hypothetical protein (NCBI) 59, 442
PA1269 PA1269 probable transcriptional regulator (NCBI) 59, 143
PA1295 PA1295 hypothetical protein (NCBI) 59, 544
PA2992 PA2992 hypothetical protein (NCBI) 43, 552
PA3640 dnaE DNA polymerase III subunit alpha (NCBI) 270, 552
PA3849 ndpA nucleoid-associated protein NdpA (NCBI) 59, 263
PA4002 rodA rod shape-determining protein (NCBI) 59, 478
PA4003 pbpA penicillin-binding protein 2 (NCBI) 204, 552
PA4116 PA4116 hypothetical protein (NCBI) 59, 195
PA4118 PA4118 hypothetical protein (NCBI) 59, 268
PA4458 PA4458 hypothetical protein (NCBI) 262, 552
PA4459 PA4459 hypothetical protein (NCBI) 262, 552
PA4769 PA4769 probable transcriptional regulator (NCBI) 59, 117
PA4856 retS regulator of exopolysaccharide and type III secretion (NCBI) 59, 552
PA4965 PA4965 hypothetical protein (NCBI) 59, 442
PA4968 PA4968 hypothetical protein (NCBI) 59, 442
PA4969 PA4969 hypothetical protein (NCBI) 59, 218
PA4970 PA4970 hypothetical protein (NCBI) 59, 368
PA5000 PA5000 probable glycosyl transferase (NCBI) 59, 296
PA5045 ponA penicillin-binding protein 1A (NCBI) 59, 91
PA5070 tatC transport protein TatC (NCBI) 75, 552
PA5077 mdoH glucosyltransferase MdoH (NCBI) 91, 552
PA5110 fbp fructose-1,6-bisphosphatase (NCBI) 59, 225
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 PA4856
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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