Organism : Pseudomonas aeruginosa | Module List :
PA4892 ureF

urease accessory protein UreF (NCBI)

CircVis
Functional Annotations (3)
Function System
Urease accessory protein UreF cog/ cog
nitrogen compound metabolic process go/ biological_process
nickel ion binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4892
(Mouseover regulator name to see its description)

PA4892 is regulated by 30 influences and regulates 0 modules.
Regulators for PA4892 ureF (30)
Regulator Module Operator
PA0207 240 tf
PA0376 240 tf
PA0527 240 tf
PA0791 240 tf
PA0815 240 tf
PA1067 240 tf
PA1125 240 tf
PA2056 240 tf
PA2118 240 tf
PA2899 240 tf
PA3594 240 tf
PA4132 240 tf
PA4169 240 tf
PA4196 240 tf
PA4890 240 tf
PA4989 240 tf
PA5293 240 tf
PA5437 240 tf
PA5562 240 tf
PA0133 44 tf
PA0279 44 tf
PA1399 44 tf
PA1467 44 tf
PA1836 44 tf
PA2047 44 tf
PA3845 44 tf
PA4270 44 tf
PA4508 44 tf
PA5116 44 tf
PA5344 44 tf

Warning: PA4892 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
2920 3.20e-16 aaTatttttc.AaATc.Aaa
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2921 3.70e-02 tGataAaGATgC..t.caCG.aaa
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3308 1.50e-02 aaaTttTt.t.taCa.c.atgTgA
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3309 3.40e+02 gCAaccatAaCaaCc.ggA
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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 PA4892

PA4892 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Urease accessory protein UreF cog/ cog
nitrogen compound metabolic process go/ biological_process
nickel ion binding go/ molecular_function
Module neighborhood information for PA4892

PA4892 has total of 44 gene neighbors in modules 44, 240
Gene neighbors (44)
Gene Common Name Description Module membership
PA0025 aroE shikimate dehydrogenase (NCBI) 240, 333
PA0164 PA0164 probable gamma-glutamyltranspeptidase (NCBI) 240, 266
PA1051 PA1051 probable transporter (NCBI) 240, 337
PA1052 PA1052 hypothetical protein (NCBI) 240, 337
PA1165 pcpS PcpS (NCBI) 44, 326
PA1399 PA1399 probable transcriptional regulator (NCBI) 44, 307
PA1400 PA1400 probable pyruvate carboxylase (NCBI) 44, 307
PA1416 PA1416 hypothetical protein (NCBI) 151, 240
PA1417 PA1417 probable decarboxylase (NCBI) 151, 240
PA1418 PA1418 probable sodium:solute symport protein (NCBI) 151, 240
PA1419 PA1419 probable transporter (NCBI) 151, 240
PA1420 PA1420 hypothetical protein (NCBI) 151, 240
PA1421 gbuA guanidinobutyrase (NCBI) 151, 240
PA1467 PA1467 hypothetical protein (NCBI) 44, 326
PA1468 PA1468 hypothetical protein (NCBI) 44, 507
PA1600 PA1600 probable cytochrome c (NCBI) 240, 546
PA1601 PA1601 probable aldehyde dehydrogenase (NCBI) 240, 546
PA1602 PA1602 probable oxidoreductase (NCBI) 240, 546
PA1836 PA1836 probable transcriptional regulator (NCBI) 44, 344
PA1885 PA1885 hypothetical protein (NCBI) 30, 44
PA2757 PA2757 hypothetical protein (NCBI) 240, 247
PA2847 PA2847 hypothetical protein (NCBI) 44, 344
PA3018 PA3018 hypothetical protein (NCBI) 240, 333
PA3035 PA3035 probable glutathione S-transferase (NCBI) 240, 377
PA3281 PA3281 hypothetical protein (NCBI) 48, 240
PA3282 PA3282 hypothetical protein (NCBI) 48, 240
PA3283 PA3283 hypothetical protein (NCBI) 48, 240
PA3284 PA3284 hypothetical protein (NCBI) 48, 240
PA3389 PA3389 probable ring-cleaving dioxygenase (NCBI) 44, 532
PA3390 PA3390 hypothetical protein (NCBI) 44, 532
PA3835 PA3835 hypothetical protein (NCBI) 44, 173
PA3845 PA3845 probable transcriptional regulator (NCBI) 44, 190
PA4382 PA4382 hypothetical protein (NCBI) 44, 537
PA4507 PA4507 hypothetical protein (NCBI) 34, 44
PA4508 PA4508 probable transcriptional regulator (NCBI) 44, 101
PA4766 PA4766 hypothetical protein (NCBI) 44, 139
PA4770 lldP L-lactate permease (NCBI) 82, 240
PA4771 lldD L-lactate dehydrogenase (NCBI) 82, 240
PA4772 PA4772 probable ferredoxin (NCBI) 82, 240
PA4891 ureE urease accessory protein UreE (NCBI) 240, 380
PA4892 ureF urease accessory protein UreF (NCBI) 44, 240
PA5116 PA5116 probable transcriptional regulator (NCBI) 44, 97
PA5211 PA5211 hypothetical protein (NCBI) 30, 44
PA5440 PA5440 probable peptidase (NCBI) 240, 333
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 PA4892
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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