Organism : Pseudomonas aeruginosa | Module List :
PA0683

probable type II secretion system protein (NCBI)

CircVis
Functional Annotations (5)
Function System
protein transporter activity go/ molecular_function
Gram-negative-bacterium-type cell wall go/ cellular_component
protein transport go/ biological_process
integral to membrane go/ cellular_component
Bacterial secretion system kegg/ kegg pathway
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA0683
(Mouseover regulator name to see its description)

PA0683 is regulated by 25 influences and regulates 0 modules.
Regulators for PA0683 (25)
Regulator Module Operator
PA0163 132 tf
PA0191 132 tf
PA0306 132 tf
PA0675 132 tf
PA0701 132 tf
PA1347 132 tf
PA1754 132 tf
PA1826 132 tf
PA1980 132 tf
PA2096 132 tf
PA2838 132 tf
PA3381 132 tf
PA3594 132 tf
PA3804 132 tf
PA4165 132 tf
PA5344 132 tf
PA5562 132 tf
PA0191 400 tf
PA0527 400 tf
PA0675 400 tf
PA0701 400 tf
PA0707 400 tf
PA2696 400 tf
PA3381 400 tf
PA5525 400 tf

Warning: PA0683 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
3094 1.40e+01 cTtggaAATCc
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3095 2.70e+03 CGGaGaCggCCgCaAgGaCcT
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3624 5.10e+01 aaagccccGcTccAgGgaCTTgc
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3625 1.20e+03 TGAcAaatctT
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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 PA0683

PA0683 is enriched for 5 functions in 4 categories.
Enrichment Table (5)
Function System
protein transporter activity go/ molecular_function
Gram-negative-bacterium-type cell wall go/ cellular_component
protein transport go/ biological_process
integral to membrane go/ cellular_component
Bacterial secretion system kegg/ kegg pathway
Module neighborhood information for PA0683

PA0683 has total of 32 gene neighbors in modules 132, 400
Gene neighbors (32)
Gene Common Name Description Module membership
PA0273 PA0273 probable major facilitator superfamily (MFS) transporter (NCBI) 25, 132
PA0466 PA0466 hypothetical protein (NCBI) 92, 132
PA0674 PA0674 hypothetical protein (NCBI) 132, 500
PA0680 PA0680 HxcV putative pseudopilin (NCBI) 105, 400
PA0681 PA0681 HxcT pseudopilin (NCBI) 132, 400
PA0682 PA0682 HxcX atypical pseudopilin (NCBI) 132, 400
PA0683 PA0683 probable type II secretion system protein (NCBI) 132, 400
PA0684 PA0684 probable type II secretion system protein (NCBI) 132, 400
PA0685 PA0685 probable type II secretion system protein (NCBI) 158, 400
PA0686 PA0686 probable type II secretion system protein (NCBI) 158, 400
PA0687 PA0687 probable type II secretion system protein (NCBI) 132, 400
PA0690 PA0690 hypothetical protein (NCBI) 400, 532
PA0695 PA0695 hypothetical protein (NCBI) 104, 400
PA0696 PA0696 hypothetical protein (NCBI) 158, 400
PA0697 PA0697 hypothetical protein (NCBI) 104, 400
PA0698 PA0698 hypothetical protein (NCBI) 321, 400
PA0699 PA0699 probable peptidyl-prolyl cis-trans isomerase, PpiC-type (NCBI) 104, 400
PA0701 PA0701 probable transcriptional regulator (NCBI) 50, 400
PA1194 PA1194 probable amino acid permease (NCBI) 68, 132
PA1907 PA1907 hypothetical protein (NCBI) 132, 486
PA1908 PA1908 probable major facilitator superfamily (MFS) transporter (NCBI) 132, 311
PA2058 PA2058 probable binding protein component of ABC transporter (NCBI) 50, 132
PA2059 PA2059 probable permease of ABC transporter (NCBI) 132, 483
PA2070 PA2070 hypothetical protein (NCBI) 132, 345
PA2689 PA2689 hypothetical protein (NCBI) 132, 201
PA2700 PA2700 probable porin (NCBI) 132, 345
PA2919 PA2919 hypothetical protein (NCBI) 132, 333
PA3279 oprP Phosphate-specific outer membrane porin OprP precursor (NCBI) 132, 439
PA3404 PA3404 probable outer membrane protein precursor (NCBI) 132, 171
PA3405 hasE metalloprotease secretion protein (NCBI) 132, 171
PA3406 hasD transport protein HasD (NCBI) 132, 289
PA4859 PA4859 probable permease of ABC transporter (NCBI) 132, 486
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 PA0683
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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