Organism : Pseudomonas aeruginosa | Module List :
PA4305

hypothetical protein (NCBI)

CircVis
Functional Annotations (2)
Function System
Flp pilus assembly protein CpaB cog/ cog
pilus_cpaB tigr/ tigrfam
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA4305
(Mouseover regulator name to see its description)

PA4305 is regulated by 26 influences and regulates 0 modules.
Regulators for PA4305 (26)
Regulator Module Operator
PA0179 54 tf
PA0707 54 tf
PA0791 54 tf
PA1109 54 tf
PA1351 54 tf
PA2897 54 tf
PA3249 54 tf
PA3269 54 tf
PA3363 54 tf
PA3583 54 tf
PA3921 54 tf
PA4296 54 tf
PA4436 54 tf
PA4703 54 tf
PA4745 54 tf
PA5059 54 tf
PA5105 54 tf
PA5344 54 tf
PA0179 200 tf
PA1351 200 tf
PA3596 200 tf
PA3921 200 tf
PA4703 200 tf
PA5059 200 tf
PA5239 200 tf
PA5344 200 tf

Warning: PA4305 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
2940 1.90e+02 A.ctAAAtgG.ATTa
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2941 1.40e+03 ATAtaA
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3228 1.60e+03 GATgaTTC
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3229 6.10e+03 AAAAcTtTAcTTT
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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 PA4305

PA4305 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Flp pilus assembly protein CpaB cog/ cog
pilus_cpaB tigr/ tigrfam
Module neighborhood information for PA4305

PA4305 has total of 30 gene neighbors in modules 54, 200
Gene neighbors (30)
Gene Common Name Description Module membership
PA0483 PA0483 probable acetyltransferase (NCBI) 153, 200
PA1190 PA1190 hypothetical protein (NCBI) 133, 200
PA1874 PA1874 hypothetical protein (NCBI) 54, 392
PA1875 PA1875 probable outer membrane protein precursor (NCBI) 54, 392
PA1876 PA1876 probable ATP-binding/permease fusion ABC transporter (NCBI) 54, 392
PA1877 PA1877 probable secretion protein (NCBI) 54, 392
PA2360 PA2360 hypothetical protein (NCBI) 73, 200
PA2361 PA2361 hypothetical protein (NCBI) 183, 200
PA2362 PA2362 hypothetical protein (NCBI) 73, 200
PA2364 PA2364 hypothetical protein (NCBI) 133, 200
PA2369 PA2369 hypothetical protein (NCBI) 183, 200
PA2371 PA2371 probable ClpA/B-type protease (NCBI) 183, 200
PA2372 PA2372 hypothetical protein (NCBI) 200, 226
PA2375 PA2375 hypothetical protein (NCBI) 133, 200
PA2430 PA2430 hypothetical protein (NCBI) 200, 519
PA2787 cpg2 glutamate carboxypepticase (NCBI) 200, 382
PA4112 PA4112 probable sensor/response regulator hybrid (NCBI) 200, 382
PA4293 PA4293 probable two-component sensor (NCBI) 54, 392
PA4294 PA4294 hypothetical protein (NCBI) 54, 159
PA4297 PA4297 hypothetical protein (NCBI) 54, 482
PA4298 PA4298 hypothetical protein (NCBI) 54, 482
PA4299 PA4299 hypothetical protein (NCBI) 54, 392
PA4300 PA4300 hypothetical protein (NCBI) 54, 482
PA4301 PA4301 hypothetical protein (NCBI) 200, 475
PA4302 PA4302 probable type II secretion system protein (NCBI) 54, 392
PA4303 PA4303 hypothetical protein (NCBI) 54, 392
PA4304 PA4304 probable type II secretion system protein (NCBI) 54, 482
PA4305 PA4305 hypothetical protein (NCBI) 54, 200
PA4306 PA4306 hypothetical protein (NCBI) 54, 503
PA5101 PA5101 hypothetical protein (NCBI) 200, 482
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 PA4305
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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