Organism : Pseudomonas aeruginosa | Module List :
PA3622 rpoS

sigma factor RpoS (NCBI)

CircVis
Functional Annotations (7)
Function System
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
rpoS_proteo tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3622
(Mouseover regulator name to see its description)

PA3622 is regulated by 45 influences and regulates 64 modules.
Regulators for PA3622 rpoS (45)
Regulator Module Operator
PA0125 413 tf
PA0179 413 tf
PA0764 413 tf
PA0797 413 tf
PA0831 413 tf
PA1197 413 tf
PA1269 413 tf
PA1422 413 tf
PA1544 413 tf
PA1760 413 tf
PA2016 413 tf
PA2047 413 tf
PA2076 413 tf
PA2277 413 tf
PA2556 413 tf
PA2622 413 tf
PA2848 413 tf
PA3225 413 tf
PA3622 413 tf
PA3776 413 tf
PA3921 413 tf
PA4052 413 tf
PA4145 413 tf
PA4354 413 tf
PA4581 413 tf
PA5157 413 tf
PA5253 413 tf
PA5337 413 tf
PA5403 413 tf
PA5438 413 tf
PA5550 413 tf
PA0120 141 tf
PA0125 141 tf
PA0167 141 tf
PA0393 141 tf
PA0797 141 tf
PA1760 141 tf
PA2047 141 tf
PA2577 141 tf
PA3622 141 tf
PA3973 141 tf
PA5253 141 tf
PA5403 141 tf
PA5437 141 tf
PA5550 141 tf

Warning: PA3622 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
3112 8.20e+01 gtTtcCtc.tCCGt..g
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3113 6.10e+04 TGaTCTTCCT
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3650 2.00e+02 ACTcAAAA
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3651 4.40e+02 aGaaGatCTcgcgcAAgGG
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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 PA3622

PA3622 is enriched for 7 functions in 3 categories.
Enrichment Table (7)
Function System
DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
transcription initiation, DNA-dependent go/ biological_process
regulation of transcription, DNA-dependent go/ biological_process
sigma factor activity go/ molecular_function
RNA polymerase kegg/ kegg pathway
rpoS_proteo tigr/ tigrfam
Module neighborhood information for PA3622

PA3622 has total of 22 gene neighbors in modules 141, 413
Gene neighbors (22)
Gene Common Name Description Module membership
PA0315 PA0315 hypothetical protein (NCBI) 141, 441
PA0446 PA0446 hypothetical protein (NCBI) 141, 523
PA0459 PA0459 probable ClpA/B protease ATP binding subunit (NCBI) 46, 413
PA0586 PA0586 hypothetical protein (NCBI) 413, 548
PA0587 PA0587 hypothetical protein (NCBI) 413, 548
PA0588 PA0588 hypothetical protein (NCBI) 413, 548
PA0744 PA0744 probable enoyl-CoA hydratase/isomerase (NCBI) 227, 413
PA0745 PA0745 enoyl-CoA hydratase (NCBI) 227, 413
PA0746 PA0746 probable acyl-CoA dehydrogenase (NCBI) 145, 413
PA0747 PA0747 probable aldehyde dehydrogenase (NCBI) 145, 413
PA0792 prpD 2-methylcitrate dehydratase (NCBI) 141, 258
PA0862 PA0862 hypothetical protein (NCBI) 63, 141
PA2047 PA2047 probable transcriptional regulator (NCBI) 141, 153
PA2709 cysK cysteine synthase A (NCBI) 95, 141
PA2915 PA2915 hypothetical protein (NCBI) 141, 208
PA3615 PA3615 hypothetical protein (NCBI) 38, 141
PA3622 rpoS sigma factor RpoS (NCBI) 141, 413
PA3848 PA3848 hypothetical protein (NCBI) 7, 141
PA3919 PA3919 hypothetical protein (NCBI) 141, 381
PA4015 PA4015 hypothetical protein (NCBI) 141, 488
PA5018 msrA peptide methionine sulfoxide reductase (NCBI) 95, 141
PA5206 argE acetylornithine deacetylase (NCBI) 141, 361
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 PA3622
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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