Organism : Pseudomonas aeruginosa | Module List :
PA4263 rplC

50S ribosomal protein L3 (NCBI)

CircVis
Functional Annotations (6)
Function System
Ribosomal protein L3 cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
L3_bact tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4263
(Mouseover regulator name to see its description)

PA4263 is regulated by 43 influences and regulates 0 modules.
Regulators for PA4263 rplC (43)
Regulator Module Operator
PA0123 539 tf
PA0163 539 tf
PA0456 539 tf
PA0564 539 tf
PA0652 539 tf
PA0739 539 tf
PA1141 539 tf
PA1374 539 tf
PA1760 539 tf
PA2387 539 tf
PA3007 539 tf
PA3184 539 tf
PA3721 539 tf
PA3778 539 tf
PA4057 539 tf
PA4238 539 tf
PA4270 539 tf
PA4275 539 tf
PA4581 539 tf
PA4659 539 tf
PA4745 539 tf
PA4853 539 tf
PA4984 539 tf
PA5125 539 tf
PA5337 539 tf
PA5437 539 tf
PA0456 13 tf
PA0652 13 tf
PA1504 13 tf
PA1776 13 tf
PA4052 13 tf
PA4057 13 tf
PA4238 13 tf
PA4269 13 tf
PA4275 13 tf
PA4279 13 tf
PA4530 13 tf
PA4745 13 tf
PA4755 13 tf
PA4853 13 tf
PA4890 13 tf
PA5125 13 tf
PA5288 13 tf

Warning: PA4263 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
2862 2.30e+02 AATTtgCa
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2863 4.80e+03 AACGAAAaGA
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3890 2.00e+02 AGTaAA
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3891 2.50e+02 ttTtccgaa.cAcAaaCcaAa
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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 PA4263

PA4263 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Ribosomal protein L3 cog/ cog
structural constituent of ribosome go/ molecular_function
ribosome go/ cellular_component
translation go/ biological_process
Ribosome kegg/ kegg pathway
L3_bact tigr/ tigrfam
Module neighborhood information for PA4263

PA4263 has total of 19 gene neighbors in modules 13, 539
Gene neighbors (19)
Gene Common Name Description Module membership
PA0966 ruvA Holliday junction DNA helicase motor protein (NCBI) 13, 69
PA0968 PA0968 hypothetical protein (NCBI) 13, 69
PA0973 oprL Peptidoglycan associated lipoprotein OprL precursor (NCBI) 13, 182
PA2967 fabG 3-oxoacyl-[acyl-carrier-protein] reductase (NCBI) 13, 256
PA3110 PA3110 hypothetical protein (NCBI) 13, 256
PA3111 folC folylpolyglutamate synthetase (NCBI) 13, 256
PA3655 tsf elongation factor Ts (NCBI) 419, 539
PA3656 rpsB 30S ribosomal protein S2 (NCBI) 419, 539
PA4263 rplC 50S ribosomal protein L3 (NCBI) 13, 539
PA4264 rpsJ 30S ribosomal protein S10 (NCBI) 210, 539
PA4265 tufA elongation factor Tu (NCBI) 19, 539
PA4266 fusA1 elongation factor G (NCBI) 13, 539
PA4267 rpsG 30S ribosomal protein S7 (NCBI) 13, 539
PA4268 rpsL 30S ribosomal protein S12 (NCBI) 19, 539
PA4271 rplL 50S ribosomal protein L7/L12 (NCBI) 419, 539
PA4272 rplJ 50S ribosomal protein L10 (NCBI) 419, 539
PA4273 rplA 50S ribosomal protein L1 (NCBI) 13, 539
PA4274 rplK 50S ribosomal protein L11 (NCBI) 13, 539
PA5569 rnpA ribonuclease P (NCBI) 13, 282
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 PA4263
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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