Organism : Pseudomonas aeruginosa | Module List :
PA2354

probable transcriptional regulator (NCBI)

CircVis
Functional Annotations (7)
Function System
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain cog/ cog
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 PA2354
(Mouseover regulator name to see its description)

PA2354 is regulated by 35 influences and regulates 15 modules.
Regulators for PA2354 (35)
Regulator Module Operator
PA0487 304 tf
PA0701 304 tf
PA1138 304 tf
PA2047 304 tf
PA2258 304 tf
PA2276 304 tf
PA2281 304 tf
PA2312 304 tf
PA2316 304 tf
PA2334 304 tf
PA2337 304 tf
PA2354 304 tf
PA2376 304 tf
PA2432 304 tf
PA2497 304 tf
PA2547 304 tf
PA2601 304 tf
PA2885 304 tf
PA3391 304 tf
PA3420 304 tf
PA3714 304 tf
PA4831 304 tf
PA5562 304 tf
PA2258 519 tf
PA2267 519 tf
PA2276 519 tf
PA2277 519 tf
PA2281 519 tf
PA2334 519 tf
PA2337 519 tf
PA2354 519 tf
PA2376 519 tf
PA2432 519 tf
PA2447 519 tf
PA2469 519 tf

Warning: PA2354 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
3434 7.10e+03 CgcctGgaCtGaCcCgC.GCc
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3435 8.60e+02 Cggt.g.gCg.gGcT.gcg
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3852 5.90e-02 ATGGgCGCcgccGcAaAA.at.cA
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3853 1.80e+00 AgTGccGaaACGcaAc.tc.G
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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 PA2354

PA2354 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
Transcriptional regulators containing an AAA-type ATPase domain and a DNA-binding domain cog/ cog
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
Module neighborhood information for PA2354

PA2354 has total of 42 gene neighbors in modules 304, 519
Gene neighbors (42)
Gene Common Name Description Module membership
PA2258 ptxR transcriptional regulator PtxR (NCBI) 290, 519
PA2267 PA2267 probable transcriptional regulator (NCBI) 62, 519
PA2268 PA2268 hypothetical protein (NCBI) 346, 519
PA2275 PA2275 probable alcohol dehydrogenase (Zn-dependent) (NCBI) 287, 519
PA2276 PA2276 probable transcriptional regulator (NCBI) 287, 519
PA2277 arsR ArsR protein (NCBI) 287, 519
PA2278 arsB ArsB protein (NCBI) 287, 519
PA2279 arsC ArsC protein (NCBI) 287, 519
PA2280 PA2280 hypothetical protein (NCBI) 287, 519
PA2283 PA2283 hypothetical protein (NCBI) 199, 304
PA2284 PA2284 hypothetical protein (NCBI) 199, 304
PA2285 PA2285 hypothetical protein (NCBI) 199, 304
PA2287 PA2287 hypothetical protein (NCBI) 199, 304
PA2313 PA2313 hypothetical protein (NCBI) 199, 304
PA2314 PA2314 probable major facilitator superfamily (MFS) transporter (NCBI) 304, 344
PA2324 PA2324 hypothetical protein (NCBI) 287, 304
PA2333 PA2333 probable sulfatase (NCBI) 199, 519
PA2338 PA2338 probable binding protein component of ABC maltose/mannitol transporter (NCBI) 475, 519
PA2339 PA2339 probable binding-protein-dependent maltose/mannitol transport protein (NCBI) 199, 304
PA2340 PA2340 probable binding-protein-dependent maltose/mannitol transport protein (NCBI) 199, 304
PA2342 mtlD mannitol dehydrogenase (NCBI) 199, 304
PA2343 mtlY xylulose kinase (NCBI) 199, 304
PA2346 PA2346 hypothetical protein (NCBI) 304, 446
PA2348 PA2348 hypothetical protein (NCBI) 285, 304
PA2352 PA2352 probable glycerophosphoryl diester phosphodiesterase (NCBI) 276, 519
PA2353 PA2353 hypothetical protein (NCBI) 291, 519
PA2354 PA2354 probable transcriptional regulator (NCBI) 304, 519
PA2355 PA2355 probable FMNH2-dependent monooxygenase (NCBI) 304, 519
PA2356 msuD methanesulfonate sulfonatase MsuD (NCBI) 304, 519
PA2377 PA2377 hypothetical protein (NCBI) 119, 519
PA2418 PA2418 hypothetical protein (NCBI) 199, 519
PA2420 PA2420 probable porin (NCBI) 199, 304
PA2429 PA2429 hypothetical protein (NCBI) 334, 519
PA2430 PA2430 hypothetical protein (NCBI) 200, 519
PA2431 PA2431 hypothetical protein (NCBI) 334, 519
PA2438 PA2438 hypothetical protein (NCBI) 446, 519
PA2465 PA2465 hypothetical protein (NCBI) 304, 519
PA2472 PA2472 probable major facilitator superfamily (MFS) transporter (NCBI) 285, 304
PA2473 PA2473 probable glutathione S-transferase (NCBI) 199, 304
PA2474 PA2474 hypothetical protein (NCBI) 285, 304
PA2496 PA2496 hypothetical protein (NCBI) 196, 519
PA2505 PA2505 probable porin (NCBI) 287, 519
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 PA2354
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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