Organism : Pseudomonas aeruginosa | Module List :
PA4196

probable two-component response regulator (NCBI)

CircVis
Functional Annotations (9)
Function System
Response regulator 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
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4196
(Mouseover regulator name to see its description)

PA4196 is regulated by 32 influences and regulates 20 modules.
Regulators for PA4196 (32)
Regulator Module Operator
PA0207 366 tf
PA0306 366 tf
PA1374 366 tf
PA1850 366 tf
PA1998 366 tf
PA2100 366 tf
PA2736 366 tf
PA2785 366 tf
PA3045 366 tf
PA3126 366 tf
PA3804 366 tf
PA3898 366 tf
PA4196 366 tf
PA0207 109 tf
PA0547 109 tf
PA0601 109 tf
PA1141 109 tf
PA1467 109 tf
PA1850 109 tf
PA1998 109 tf
PA2316 109 tf
PA2488 109 tf
PA2556 109 tf
PA2696 109 tf
PA2758 109 tf
PA3594 109 tf
PA3778 109 tf
PA3921 109 tf
PA3932 109 tf
PA4196 109 tf
PA4787 109 tf
PA5344 109 tf

Warning: PA4196 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
3050 2.90e+01 AAgtTttTtgTataAaTaCaa
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3051 3.50e-02 ATgA.Aaaaa.gAAt
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3556 2.70e-12 tTat.tgaaaTtaata..aaa.ga
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3557 2.70e-02 AATAAAggGCGtCAAtCaaa
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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 PA4196

PA4196 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Response regulator 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
intracellular go/ cellular_component
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for PA4196

PA4196 has total of 42 gene neighbors in modules 109, 366
Gene neighbors (42)
Gene Common Name Description Module membership
PA0127 PA0127 hypothetical protein (NCBI) 109, 516
PA0207 PA0207 probable transcriptional regulator (NCBI) 355, 366
PA0346 PA0346 hypothetical protein (NCBI) 109, 355
PA0694 exbD2 transport protein ExbD (NCBI) 109, 516
PA1187 PA1187 probable acyl-CoA dehydrogenase (NCBI) 366, 439
PA1786 PA1786 hypothetical protein (NCBI) 311, 366
PA1827 PA1827 probable short-chain dehydrogenase (NCBI) 366, 463
PA1850 PA1850 probable transcriptional regulator (NCBI) 109, 326
PA1865 PA1865 hypothetical protein (NCBI) 366, 546
PA1866 PA1866 hypothetical protein (NCBI) 366, 546
PA1873 PA1873 hypothetical protein (NCBI) 109, 516
PA1883 PA1883 probable NADH-ubiquinone/plastoquinone oxidoreductase (NCBI) 109, 307
PA1910 PA1910 probable tonB-dependent receptor protein (NCBI) 109, 516
PA1928 rimJ ribosomal protein alanine acetyltransferase (NCBI) 109, 366
PA1998 PA1998 probable transcriptional regulator (NCBI) 109, 366
PA2041 PA2041 probable amino acid permease (NCBI) 80, 366
PA2100 PA2100 probable transcriptional regulator (NCBI) 80, 366
PA2101 PA2101 hypothetical protein (NCBI) 80, 366
PA2102 PA2102 hypothetical protein (NCBI) 80, 366
PA2200 PA2200 hypothetical protein (NCBI) 109, 289
PA2549 PA2549 hypothetical protein (NCBI) 109, 516
PA2589 PA2589 hypothetical protein (NCBI) 307, 366
PA2597 PA2597 hypothetical protein (NCBI) 109, 301
PA2599 PA2599 hypothetical protein (NCBI) 109, 301
PA2600 PA2600 hypothetical protein (NCBI) 93, 109
PA2736 PA2736 hypothetical protein (NCBI) 168, 366
PA2784 PA2784 hypothetical protein (NCBI) 326, 366
PA2785 PA2785 hypothetical protein (NCBI) 326, 366
PA3207 PA3207 hypothetical protein (NCBI) 295, 366
PA3230 PA3230 hypothetical protein (NCBI) 108, 109
PA3318 PA3318 hypothetical protein (NCBI) 295, 366
PA3373 PA3373 hypothetical protein (NCBI) 109, 295
PA4181 PA4181 hypothetical protein (NCBI) 109, 289
PA4196 PA4196 probable two-component response regulator (NCBI) 109, 366
PA4197 PA4197 probable two-component sensor (NCBI) 61, 366
PA4198 PA4198 acyl-CoA synthase (NCBI) 61, 366
PA4365 PA4365 probable transporter (NCBI) 109, 463
PA4660 phr deoxyribodipyrimidine photolyase (NCBI) 109, 546
PA4712 PA4712 hypothetical protein (NCBI) 109, 516
PA5020 PA5020 probable acyl-CoA dehydrogenase (NCBI) 53, 366
PA5160 PA5160 drug efflux transporter (NCBI) 366, 473
PA5228 PA5228 hypothetical protein (NCBI) 109, 229
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 PA4196
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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