Organism : Pseudomonas aeruginosa | Module List :
PA4544 rluD

pseudouridine synthase (NCBI)

CircVis
Functional Annotations (5)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4544
(Mouseover regulator name to see its description)

PA4544 is regulated by 35 influences and regulates 0 modules.
Regulators for PA4544 rluD (35)
Regulator Module Operator
PA0120 404 tf
PA0125 404 tf
PA1159 404 tf
PA1359 404 tf
PA1422 404 tf
PA1520 404 tf
PA2047 404 tf
PA2622 404 tf
PA2957 404 tf
PA3135 404 tf
PA3604 404 tf
PA3622 404 tf
PA4052 404 tf
PA4451 404 tf
PA4745 404 tf
PA4853 404 tf
PA5239 404 tf
PA5253 404 tf
PA5550 404 tf
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

Warning: PA4544 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
3632 1.80e+00 TAagAT.cgCgaCCcTtgaa.acc
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3633 2.00e-01 AAaGCaaagcctccGAgCggAAA
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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 PA4544

PA4544 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Pseudouridylate synthases, 23S RNA-specific cog/ cog
pseudouridine synthesis go/ biological_process
RNA binding go/ molecular_function
pseudouridine synthase activity go/ molecular_function
rluA_subfam tigr/ tigrfam
Module neighborhood information for PA4544

PA4544 has total of 24 gene neighbors in modules 404, 424
Gene neighbors (24)
Gene Common Name Description Module membership
PA0373 ftsY signal recognition particle receptor FtsY (NCBI) 424, 552
PA0577 dnaG DNA primase (NCBI) 404, 474
PA0578 PA0578 hypothetical protein (NCBI) 404, 474
PA0580 gcp O-sialoglycoprotein endopeptidase (NCBI) 230, 404
PA0858 PA0858 hypothetical protein (NCBI) 114, 404
PA2840 PA2840 probable ATP-dependent RNA helicase (NCBI) 404, 412
PA3179 PA3179 hypothetical protein (NCBI) 404, 528
PA3604 PA3604 probable two-component response regulator (NCBI) 255, 424
PA3621 fdxA ferredoxin I (NCBI) 354, 424
PA3741 PA3741 hypothetical protein (NCBI) 404, 501
PA3817 PA3817 probable methyltransferase (NCBI) 354, 424
PA3818 PA3818 extragenic suppressor protein SuhB (NCBI) 230, 404
PA3824 queA S-adenosylmethionine:tRNA ribosyltransferase-isomerase (NCBI) 404, 520
PA3966 PA3966 hypothetical protein (NCBI) 354, 424
PA4451 PA4451 hypothetical protein (NCBI) 354, 424
PA4544 rluD pseudouridine synthase (NCBI) 404, 424
PA4566 obg GTP-binding protein Obg (NCBI) 352, 424
PA4746 PA4746 hypothetical protein (NCBI) 354, 424
PA4748 tpiA triosephosphate isomerase (NCBI) 404, 474
PA4852 PA4852 hypothetical protein (NCBI) 424, 474
PA4940 PA4940 hypothetical protein (NCBI) 424, 440
PA5118 thiI thiamine biosynthesis protein ThiI (NCBI) 56, 404
PA5286 PA5286 hypothetical protein (NCBI) 354, 424
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 PA4544
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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