Organism : Pseudomonas aeruginosa | Module List :
PA4052 nusB

transcription antitermination protein NusB (NCBI)

CircVis
Functional Annotations (9)
Function System
Transcription termination factor cog/ cog
transcription termination factor activity go/ molecular_function
RNA binding go/ molecular_function
transcription termination, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
zinc ion binding go/ molecular_function
nusB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4052
(Mouseover regulator name to see its description)

PA4052 is regulated by 35 influences and regulates 59 modules.
Regulators for PA4052 nusB (35)
Regulator Module Operator
PA0393 77 tf
PA0455 77 tf
PA1347 77 tf
PA1776 77 tf
PA2047 77 tf
PA2957 77 tf
PA3002 77 tf
PA3381 77 tf
PA3604 77 tf
PA3757 77 tf
PA3965 77 tf
PA4052 77 tf
PA4238 77 tf
PA4275 77 tf
PA4451 77 tf
PA4530 77 tf
PA4745 77 tf
PA4755 77 tf
PA4787 77 tf
PA5274 77 tf
PA0893 99 tf
PA0961 99 tf
PA1300 99 tf
PA1363 99 tf
PA1853 99 tf
PA2849 99 tf
PA3622 99 tf
PA3899 99 tf
PA4052 99 tf
PA4275 99 tf
PA4451 99 tf
PA4853 99 tf
PA5059 99 tf
PA5403 99 tf
PA5550 99 tf

Warning: PA4052 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
2986 5.30e-01 TCGtTaAAAa
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2987 9.00e+01 AagCaaAAAcc
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3030 4.10e+00 aaatttgaaaAgCatTatcaTtT
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3031 5.60e+03 AAAcAG
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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 PA4052

PA4052 is enriched for 9 functions in 3 categories.
Enrichment Table (9)
Function System
Transcription termination factor cog/ cog
transcription termination factor activity go/ molecular_function
RNA binding go/ molecular_function
transcription termination, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
proteolysis go/ biological_process
metallopeptidase activity go/ molecular_function
zinc ion binding go/ molecular_function
nusB tigr/ tigrfam
Module neighborhood information for PA4052

PA4052 has total of 30 gene neighbors in modules 77, 99
Gene neighbors (30)
Gene Common Name Description Module membership
PA0150 PA0150 probable transmembrane sensor (NCBI) 99, 247
PA0800 PA0800 hypothetical protein (NCBI) 99, 117
PA0801 PA0801 hypothetical protein (NCBI) 99, 187
PA0802 PA0802 hypothetical protein (NCBI) 99, 117
PA0949 wrbA Trp repressor binding protein WrbA (NCBI) 77, 214
PA0950 PA0950 probable arsenate reductase (NCBI) 77, 214
PA1037 PA1037 hypothetical protein (NCBI) 65, 99
PA1363 PA1363 probable sigma-70 factor, ECF subfamily (NCBI) 99, 550
PA1364 PA1364 probable transmembrane sensor (NCBI) 99, 550
PA1365 PA1365 probable siderophore receptor (NCBI) 99, 119
PA2626 trmU tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase (NCBI) 77, 395
PA2666 PA2666 probable 6-pyruvoyl tetrahydrobiopterin synthase (NCBI) 99, 261
PA2761 PA2761 hypothetical protein (NCBI) 99, 218
PA2968 fabD malonyl-CoA-[acyl-carrier-protein] transacylase (NCBI) 77, 256
PA2999 nqrA Na(+)-translocating NADH-quinone reductase subunit A (NCBI) 77, 395
PA3268 PA3268 probable TonB-dependent receptor (NCBI) 98, 99
PA3639 accA acetyl-CoA carboxylase alpha subunit (NCBI) 77, 178
PA3665 PA3665 hypothetical protein (NCBI) 99, 440
PA4048 PA4048 hypothetical protein (NCBI) 99, 387
PA4051 thiL thiamine monophosphate kinase (NCBI) 99, 387
PA4052 nusB transcription antitermination protein NusB (NCBI) 77, 99
PA4053 ribH riboflavin synthase subunit beta (NCBI) 77, 395
PA4055 ribC riboflavin synthase subunit alpha (NCBI) 77, 130
PA4675 PA4675 probable TonB-dependent receptor (NCBI) 98, 99
PA4939 PA4939 ATP phosphoribosyltransferase regulatory subunit (NCBI) 77, 478
PA5235 glpT glycerol-3-phosphate transporter (NCBI) 99, 358
PA5274 rnk nucleoside diphosphate kinase regulator (NCBI) 77, 178
PA5402 PA5402 hypothetical protein (NCBI) 92, 99
PA5403 PA5403 probable transcriptional regulator (NCBI) 58, 99
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 PA4052
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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