Organism : Pseudomonas aeruginosa | Module List :
PA0641

probable bacteriophage protein (NCBI)

CircVis
Functional Annotations (5)
Function System
Phage-related protein, tail component cog/ cog
hydrolase activity, hydrolyzing O-glycosyl compounds go/ molecular_function
extracellular region go/ cellular_component
carbohydrate metabolic process go/ biological_process
carbohydrate binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0641
(Mouseover regulator name to see its description)

PA0641 is regulated by 50 influences and regulates 0 modules.
Regulators for PA0641 (50)
Regulator Module Operator
PA0116 96 tf
PA0610 96 tf
PA0611 96 tf
PA0815 96 tf
PA0839 96 tf
PA0876 96 tf
PA0906 96 tf
PA0942 96 tf
PA1197 96 tf
PA1413 96 tf
PA1603 96 tf
PA1713 96 tf
PA1998 96 tf
PA2032 96 tf
PA2126 96 tf
PA2196 96 tf
PA2921 96 tf
PA2957 96 tf
PA3574 96 tf
PA3721 96 tf
PA4755 96 tf
PA5274 96 tf
PA5283 96 tf
PA5525 96 tf
PA0116 149 tf
PA0610 149 tf
PA0611 149 tf
PA0815 149 tf
PA0876 149 tf
PA0906 149 tf
PA1099 149 tf
PA1223 149 tf
PA1261 149 tf
PA1351 149 tf
PA1413 149 tf
PA1603 149 tf
PA1713 149 tf
PA2126 149 tf
PA2196 149 tf
PA2718 149 tf
PA2957 149 tf
PA3002 149 tf
PA3721 149 tf
PA4755 149 tf
PA4784 149 tf
PA5274 149 tf
PA5283 149 tf
PA5437 149 tf
PA5438 149 tf
PA5525 149 tf

Warning: PA0641 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
3024 1.20e+01 GtCaTtTT
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3025 1.40e+02 ttct.cgcaTgaaGgAgcG
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3128 1.10e-02 tCATcCa.AaAAAGg
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3129 6.40e+03 CTTTTT
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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 PA0641

PA0641 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Phage-related protein, tail component cog/ cog
hydrolase activity, hydrolyzing O-glycosyl compounds go/ molecular_function
extracellular region go/ cellular_component
carbohydrate metabolic process go/ biological_process
carbohydrate binding go/ molecular_function
Module neighborhood information for PA0641

PA0641 has total of 18 gene neighbors in modules 96, 149
Gene neighbors (18)
Gene Common Name Description Module membership
PA0612 PA0612 hypothetical protein (NCBI) 11, 96
PA0614 PA0614 hypothetical protein (NCBI) 96, 149
PA0629 PA0629 hypothetical protein (NCBI) 96, 149
PA0630 PA0630 hypothetical protein (NCBI) 11, 96
PA0631 PA0631 hypothetical protein (NCBI) 96, 149
PA0632 PA0632 hypothetical protein (NCBI) 96, 149
PA0633 PA0633 hypothetical protein (NCBI) 96, 149
PA0634 PA0634 hypothetical protein (NCBI) 96, 149
PA0635 PA0635 hypothetical protein (NCBI) 96, 149
PA0636 PA0636 hypothetical protein (NCBI) 96, 149
PA0637 PA0637 hypothetical protein (NCBI) 96, 149
PA0638 PA0638 probable bacteriophage protein (NCBI) 96, 149
PA0639 PA0639 hypothetical protein (NCBI) 96, 149
PA0640 PA0640 probable bacteriophage protein (NCBI) 11, 96
PA0641 PA0641 probable bacteriophage protein (NCBI) 96, 149
PA0807 PA0807 hypothetical protein (NCBI) 96, 149
PA0910 PA0910 hypothetical protein (NCBI) 11, 149
PA0911 PA0911 hypothetical protein (NCBI) 96, 149
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 PA0641
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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