Organism : Pseudomonas aeruginosa | Module List :
PA3727

hypothetical protein (NCBI)

CircVis
Functional Annotations (2)
Function System
catalytic activity go/ molecular_function
metabolic process go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3727
(Mouseover regulator name to see its description)

PA3727 is regulated by 67 influences and regulates 0 modules.
Regulators for PA3727 (67)
Regulator Module Operator
PA0167 76 tf
PA0610 76 tf
PA0876 76 tf
PA0905 76 tf
PA1226 76 tf
PA1241 76 tf
PA1290 76 tf
PA1397 76 tf
PA1526 76 tf
PA1544 76 tf
PA1633 76 tf
PA1663 76 tf
PA1760 76 tf
PA2258 76 tf
PA2426 76 tf
PA2622 76 tf
PA2718 76 tf
PA2877 76 tf
PA3135 76 tf
PA3571 76 tf
PA3711 76 tf
PA4074 76 tf
PA4080 76 tf
PA4296 76 tf
PA4354 76 tf
PA4436 76 tf
PA4462 76 tf
PA4508 76 tf
PA4769 76 tf
PA5157 76 tf
PA5166 76 tf
PA5356 76 tf
PA5438 76 tf
PA5483 76 tf
PA0610 45 tf
PA0611 45 tf
PA0708 45 tf
PA0873 45 tf
PA0876 45 tf
PA1015 45 tf
PA1128 45 tf
PA1226 45 tf
PA1315 45 tf
PA1351 45 tf
PA1544 45 tf
PA1633 45 tf
PA1663 45 tf
PA1760 45 tf
PA2258 45 tf
PA2354 45 tf
PA2426 45 tf
PA2622 45 tf
PA2877 45 tf
PA3699 45 tf
PA3757 45 tf
PA3845 45 tf
PA3921 45 tf
PA3948 45 tf
PA4296 45 tf
PA4354 45 tf
PA4462 45 tf
PA4769 45 tf
PA4914 45 tf
PA5356 45 tf
PA5438 45 tf
PA5483 45 tf
PA5550 45 tf

Warning: PA3727 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
2922 2.00e+02 Ca.aaGGAggagg.C
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2923 1.10e+04 attGcggca.cagGc.g.gcCGcg
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2984 1.40e+01 acAAGGA
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2985 5.70e+02 CCgGCgcC.GGCGGAT.ctGC
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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 PA3727

PA3727 is enriched for 2 functions in 2 categories.
Enrichment Table (2)
Function System
catalytic activity go/ molecular_function
metabolic process go/ biological_process
Module neighborhood information for PA3727

PA3727 has total of 33 gene neighbors in modules 45, 76
Gene neighbors (33)
Gene Common Name Description Module membership
PA0086 PA0086 hypothetical protein (NCBI) 45, 495
PA0087 PA0087 hypothetical protein (NCBI) 45, 495
PA0088 PA0088 hypothetical protein (NCBI) 45, 495
PA0089 PA0089 hypothetical protein (NCBI) 45, 495
PA0090 PA0090 probable ClpA/B-type chaperone (NCBI) 45, 495
PA0091 PA0091 hypothetical protein (NCBI) 45, 495
PA0126 PA0126 hypothetical protein (NCBI) 45, 76
PA0659 PA0659 hypothetical protein (NCBI) 62, 76
PA1845 PA1845 hypothetical protein (NCBI) 45, 268
PA2536 PA2536 probable phosphatidate cytidylyltransferase (NCBI) 76, 487
PA2537 PA2537 probable acyltransferase (NCBI) 76, 487
PA2538 PA2538 hypothetical protein (NCBI) 76, 487
PA2540 PA2540 hypothetical protein (NCBI) 76, 487
PA2581 PA2581 hypothetical protein (NCBI) 45, 265
PA2684 PA2684 hypothetical protein (NCBI) 66, 76
PA2685 PA2685 hypothetical protein (NCBI) 45, 431
PA2702 PA2702 hypothetical protein (NCBI) 45, 76
PA2703 PA2703 hypothetical protein (NCBI) 45, 76
PA2774 PA2774 hypothetical protein (NCBI) 45, 265
PA2775 PA2775 hypothetical protein (NCBI) 45, 265
PA2793 PA2793 hypothetical protein (NCBI) 45, 265
PA3021 PA3021 hypothetical protein (NCBI) 11, 76
PA3484 PA3484 hypothetical protein (NCBI) 45, 76
PA3485 PA3485 hypothetical protein (NCBI) 45, 76
PA3727 PA3727 hypothetical protein (NCBI) 45, 76
PA3728 PA3728 hypothetical protein (NCBI) 76, 487
PA3729 PA3729 hypothetical protein (NCBI) 76, 487
PA4487 PA4487 hypothetical protein (NCBI) 66, 76
PA4489 PA4489 hypothetical protein (NCBI) 66, 76
PA4490 PA4490 hypothetical protein (NCBI) 66, 76
PA4491 PA4491 hypothetical protein (NCBI) 66, 76
PA4492 PA4492 hypothetical protein (NCBI) 66, 76
PA5113 PA5113 hypothetical protein (NCBI) 66, 76
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 PA3727
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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