Organism : Pseudomonas aeruginosa | Module List :
PA5393

hypothetical protein (NCBI)

CircVis
Functional Annotations (4)
Function System
Predicted flavoprotein involved in K+ transport cog/ cog
monooxygenase activity go/ molecular_function
electron transport go/ biological_process
cellular aromatic compound metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA5393
(Mouseover regulator name to see its description)

PA5393 is regulated by 42 influences and regulates 0 modules.
Regulators for PA5393 (42)
Regulator Module Operator
PA0163 177 tf
PA0191 177 tf
PA0268 177 tf
PA0491 177 tf
PA0701 177 tf
PA1136 177 tf
PA1347 177 tf
PA1980 177 tf
PA2047 177 tf
PA2838 177 tf
PA3133 177 tf
PA3381 177 tf
PA3420 177 tf
PA3711 177 tf
PA3714 177 tf
PA3771 177 tf
PA3776 177 tf
PA4165 177 tf
PA4341 177 tf
PA4547 177 tf
PA5032 177 tf
PA5562 177 tf
PA0032 267 tf
PA0163 267 tf
PA0393 267 tf
PA0564 267 tf
PA0701 267 tf
PA0893 267 tf
PA1261 267 tf
PA1347 267 tf
PA1430 267 tf
PA1949 267 tf
PA1980 267 tf
PA2758 267 tf
PA2838 267 tf
PA3133 267 tf
PA3381 267 tf
PA3391 267 tf
PA3420 267 tf
PA3776 267 tf
PA5032 267 tf
PA5293 267 tf

Warning: PA5393 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
3182 7.10e-02 acctAcAAtaACaaccAga
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3183 2.40e+02 AAtTTgaCaATa
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3362 2.00e-08 aACAAgAAcaa
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3363 2.30e+03 AgcatTTCtaTA.TcaCc
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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 PA5393

PA5393 is enriched for 4 functions in 3 categories.
Enrichment Table (4)
Function System
Predicted flavoprotein involved in K+ transport cog/ cog
monooxygenase activity go/ molecular_function
electron transport go/ biological_process
cellular aromatic compound metabolic process go/ biological_process
Module neighborhood information for PA5393

PA5393 has total of 46 gene neighbors in modules 177, 267
Gene neighbors (46)
Gene Common Name Description Module membership
PA0137 PA0137 probable permease of ABC transporter (NCBI) 177, 481
PA0190 PA0190 probable acid phosphatase (NCBI) 105, 267
PA0322 PA0322 probable transporter (NCBI) 267, 337
PA0323 PA0323 probable binding protein component of ABC transporter (NCBI) 267, 310
PA0324 PA0324 probable permease of ABC transporter (NCBI) 267, 310
PA0325 PA0325 probable permease of ABC transporter (NCBI) 267, 532
PA0326 PA0326 probable ATP-binding component of ABC transporter (NCBI) 267, 532
PA0349 PA0349 hypothetical protein (NCBI) 25, 267
PA0790 PA0790 hypothetical protein (NCBI) 177, 311
PA1236 PA1236 probable major facilitator superfamily (MFS) transporter (NCBI) 16, 177
PA1238 PA1238 probable outer membrane component of multidrug efflux pump (NCBI) 177, 386
PA1262 PA1262 probable major facilitator superfamily (MFS) transporter (NCBI) 267, 408
PA1313 PA1313 probable major facilitator superfamily (MFS) transporter (NCBI) 148, 177
PA1598 PA1598 3-methyl-2-oxobutanoate hydroxymethyltransferase (NCBI) 206, 267
PA1632 kdpF KdpF protein (NCBI) 267, 319
PA1634 kdpB potassium-transporting ATPase, B chain (NCBI) 267, 319
PA1635 kdpC potassium-transporting ATPase subunit C (NCBI) 192, 267
PA1783 nasA nitrate transporter (NCBI) 12, 177
PA1974 PA1974 hypothetical protein (NCBI) 267, 459
PA1976 PA1976 probable two-component sensor (NCBI) 267, 459
PA4038 PA4038 hypothetical protein (NCBI) 192, 267
PA4098 PA4098 probable short-chain dehydrogenase (NCBI) 177, 534
PA4137 PA4137 probable porin (NCBI) 36, 177
PA4148 PA4148 probable short-chain dehydrogenase (NCBI) 177, 481
PA4149 PA4149 hypothetical protein (NCBI) 177, 481
PA4150 PA4150 probable dehydrogenase E1 component (NCBI) 177, 481
PA4151 acoB acetoin catabolism protein AcoB (NCBI) 177, 481
PA4152 PA4152 probable hydrolase (NCBI) 177, 481
PA4153 PA4153 2,3-butanediol dehydrogenase (NCBI) 177, 481
PA4187 PA4187 probable major facilitator superfamily (MFS) transporter (NCBI) 125, 267
PA4188 PA4188 hypothetical protein (NCBI) 125, 267
PA4189 PA4189 probable aldehyde dehydrogenase (NCBI) 125, 267
PA4287 PA4287 hypothetical protein (NCBI) 177, 192
PA4654 PA4654 probable major facilitator superfamily (MFS) transporter (NCBI) 267, 288
PA4804 PA4804 probable amino acid permease (NCBI) 175, 267
PA4813 lipC lipase LipC (NCBI) 105, 267
PA4860 PA4860 probable permease of ABC transporter (NCBI) 158, 267
PA4861 PA4861 probable ATP-binding component of ABC transporter (NCBI) 177, 386
PA4904 vanA vanillate O-demethylase oxygenase subunit (NCBI) 177, 323
PA4905 vanB vanillate O-demethylase oxidoreductase (NCBI) 50, 177
PA5144 PA5144 hypothetical protein (NCBI) 177, 401
PA5385 PA5385 hypothetical protein (NCBI) 177, 463
PA5390 PA5390 acetylornithine deacetylase (NCBI) 267, 481
PA5391 PA5391 hypothetical protein (NCBI) 267, 394
PA5392 PA5392 hypothetical protein (NCBI) 158, 267
PA5393 PA5393 hypothetical protein (NCBI) 177, 267
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 PA5393
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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