Organism : Pseudomonas aeruginosa | Module List :
PA3604

probable two-component response regulator (NCBI)

CircVis
Functional Annotations (9)
Function System
Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain 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 PA3604
(Mouseover regulator name to see its description)

PA3604 is regulated by 38 influences and regulates 73 modules.
Regulators for PA3604 (38)
Regulator Module Operator
PA0123 424 tf
PA0125 424 tf
PA0236 424 tf
PA0456 424 tf
PA2047 424 tf
PA2692 424 tf
PA2957 424 tf
PA3266 424 tf
PA3604 424 tf
PA4275 424 tf
PA4451 424 tf
PA4745 424 tf
PA4764 424 tf
PA4853 424 tf
PA5403 424 tf
PA5438 424 tf
PA0125 255 tf
PA0253 255 tf
PA0306 255 tf
PA0455 255 tf
PA1241 255 tf
PA1422 255 tf
PA1633 255 tf
PA2047 255 tf
PA2115 255 tf
PA2337 255 tf
PA2766 255 tf
PA2957 255 tf
PA3135 255 tf
PA3364 255 tf
PA3594 255 tf
PA3604 255 tf
PA3622 255 tf
PA3921 255 tf
PA4451 255 tf
PA4853 255 tf
PA4890 255 tf
PA5437 255 tf

Warning: PA3604 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
3338 6.30e-03 taca.Tg.gCacccTtTtCgg
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3339 4.50e+03 AaAAGCAA
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3668 3.90e+01 TtatAaAaAgC
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3669 3.00e+03 CcgCaaCCgGttTtTCAgg
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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 PA3604

PA3604 is enriched for 9 functions in 3 categories.
Module neighborhood information for PA3604

PA3604 has total of 30 gene neighbors in modules 255, 424
Gene neighbors (30)
Gene Common Name Description Module membership
PA0277 PA0277 hypothetical protein (NCBI) 255, 265
PA0358 PA0358 hypothetical protein (NCBI) 181, 255
PA0373 ftsY signal recognition particle receptor FtsY (NCBI) 424, 552
PA0947 PA0947 hypothetical protein (NCBI) 135, 255
PA1439 PA1439 hypothetical protein (NCBI) 181, 255
PA1675 PA1675 hypothetical protein (NCBI) 135, 255
PA2528 PA2528 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 255, 309
PA2850 ohr organic hydroperoxide resistance protein (NCBI) 189, 255
PA3135 PA3135 probable transcriptional regulator (NCBI) 138, 255
PA3276 PA3276 hypothetical protein (NCBI) 255, 266
PA3604 PA3604 probable two-component response regulator (NCBI) 255, 424
PA3621 fdxA ferredoxin I (NCBI) 354, 424
PA3817 PA3817 probable methyltransferase (NCBI) 354, 424
PA3966 PA3966 hypothetical protein (NCBI) 354, 424
PA3990 PA3990 hypothetical protein (NCBI) 255, 299
PA4451 PA4451 hypothetical protein (NCBI) 354, 424
PA4512 lpxO1 lipopolysaccharide biosynthetic protein LpxO1 (NCBI) 181, 255
PA4544 rluD pseudouridine synthase (NCBI) 404, 424
PA4566 obg GTP-binding protein Obg (NCBI) 352, 424
PA4746 PA4746 hypothetical protein (NCBI) 354, 424
PA4768 smpB SsrA-binding protein (NCBI) 255, 474
PA4840 PA4840 hypothetical protein (NCBI) 230, 255
PA4851 PA4851 hypothetical protein (NCBI) 181, 255
PA4852 PA4852 hypothetical protein (NCBI) 424, 474
PA4923 PA4923 hypothetical protein (NCBI) 255, 517
PA4930 alr biosynthetic alanine racemase (NCBI) 181, 255
PA4940 PA4940 hypothetical protein (NCBI) 424, 440
PA5286 PA5286 hypothetical protein (NCBI) 354, 424
PA5472 PA5472 hypothetical protein (NCBI) 247, 255
PA5491 PA5491 probable cytochrome (NCBI) 77, 424
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 PA3604
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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