Organism : Pseudomonas aeruginosa | Module List :
PA3045

probable two-component response regulator (NCBI)

CircVis
Functional Annotations (8)
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
regulation of transcription, DNA-dependent go/ biological_process
sequence-specific DNA binding go/ molecular_function
Two-component system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3045
(Mouseover regulator name to see its description)

PA3045 is regulated by 34 influences and regulates 53 modules.
Regulators for PA3045 (34)
Regulator Module Operator
PA0133 105 tf
PA0306 105 tf
PA0675 105 tf
PA0893 105 tf
PA1109 105 tf
PA1980 105 tf
PA2838 105 tf
PA3045 105 tf
PA3133 105 tf
PA3381 105 tf
PA3420 105 tf
PA3714 105 tf
PA4341 105 tf
PA4878 105 tf
PA4989 105 tf
PA5032 105 tf
PA5344 105 tf
PA5562 105 tf
PA0207 385 tf
PA0243 385 tf
PA0393 385 tf
PA0701 385 tf
PA0979 385 tf
PA1067 385 tf
PA1153 385 tf
PA1359 385 tf
PA1961 385 tf
PA2100 385 tf
PA2206 385 tf
PA2227 385 tf
PA2736 385 tf
PA3045 385 tf
PA3133 385 tf
PA3711 385 tf

Warning: PA3045 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
3042 5.90e+00 attggcAAGaAcaAc
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3043 1.30e+03 CTtTcGgcGaacT
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3594 6.60e-04 tTt.t.ttttcagT.aAtgtcatg
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3595 1.10e+01 ttgaAGTT
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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 PA3045

PA3045 is enriched for 8 functions in 3 categories.
Module neighborhood information for PA3045

PA3045 has total of 37 gene neighbors in modules 105, 385
Gene neighbors (37)
Gene Common Name Description Module membership
PA0190 PA0190 probable acid phosphatase (NCBI) 105, 267
PA0347 glpQ glycerophosphoryl diester phosphodiesterase, periplasmic (NCBI) 105, 192
PA0680 PA0680 HxcV putative pseudopilin (NCBI) 105, 400
PA0692 PA0692 hypothetical protein (NCBI) 105, 158
PA0738 PA0738 hypothetical protein (NCBI) 105, 407
PA0981 PA0981 hypothetical protein (NCBI) 231, 385
PA0992 cupC1 fimbrial subunit CupC1 (NCBI) 231, 385
PA0993 cupC2 chaperone CupC2 (NCBI) 25, 385
PA1381 PA1381 hypothetical protein (NCBI) 254, 385
PA1382 PA1382 probable type II secretion system protein (NCBI) 303, 385
PA1384 galE UDP-glucose 4-epimerase (NCBI) 254, 385
PA1385 PA1385 probable glycosyl transferase (NCBI) 254, 385
PA1386 PA1386 probable ATP-binding component of ABC transporter (NCBI) 254, 385
PA1387 PA1387 hypothetical protein (NCBI) 324, 385
PA1388 PA1388 hypothetical protein (NCBI) 324, 385
PA1389 PA1389 probable glycosyl transferase (NCBI) 324, 385
PA1393 cysC adenosine 5'-phosphosulfate (APS) kinase (NCBI) 254, 385
PA1497 PA1497 probable transporter (NCBI) 105, 201
PA1952 PA1952 hypothetical protein (NCBI) 105, 180
PA1954 PA1954 hypothetical protein (NCBI) 105, 532
PA1983 exaB cytochrome c550 (NCBI) 105, 459
PA2224 PA2224 hypothetical protein (NCBI) 188, 385
PA2225 PA2225 hypothetical protein (NCBI) 188, 385
PA2226 PA2226 hypothetical protein (NCBI) 188, 385
PA2227 PA2227 probable transcriptional regulator (NCBI) 188, 385
PA2228 PA2228 hypothetical protein (NCBI) 188, 385
PA2791 PA2791 hypothetical protein (NCBI) 340, 385
PA3044 PA3044 probable two-component sensor (NCBI) 105, 323
PA3045 PA3045 probable two-component response regulator (NCBI) 105, 385
PA3136 PA3136 probable secretion protein (NCBI) 105, 434
PA3516 PA3516 probable lyase (NCBI) 105, 407
PA3517 PA3517 probable lyase (NCBI) 105, 407
PA3518 PA3518 hypothetical protein (NCBI) 105, 407
PA3521 PA3521 probable outer membrane protein precursor (NCBI) 105, 407
PA3522 PA3522 probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI) 105, 407
PA3523 PA3523 probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI) 105, 407
PA4813 lipC lipase LipC (NCBI) 105, 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 PA3045
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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