Organism : Pseudomonas aeruginosa | Module List :
PA3692

probable outer membrane protein precursor (NCBI)

CircVis
Functional Annotations (3)
Function System
Outer membrane protein and related peptidoglycan-associated (lipo)proteins cog/ cog
cell outer membrane go/ cellular_component
integral to membrane go/ cellular_component
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for PA3692
(Mouseover regulator name to see its description)

PA3692 is regulated by 50 influences and regulates 0 modules.
Regulators for PA3692 (50)
Regulator Module Operator
PA0155 504 tf
PA0376 504 tf
PA0763 504 tf
PA0764 504 tf
PA0876 504 tf
PA0939 504 tf
PA0961 504 tf
PA1223 504 tf
PA1713 504 tf
PA1998 504 tf
PA2005 504 tf
PA2387 504 tf
PA2484 504 tf
PA2622 504 tf
PA2665 504 tf
PA2896 504 tf
PA3341 504 tf
PA3714 504 tf
PA3815 504 tf
PA4145 504 tf
PA4185 504 tf
PA4581 504 tf
PA4745 504 tf
PA4853 504 tf
PA4890 504 tf
PA5253 504 tf
PA5261 504 tf
PA5337 504 tf
PA5483 504 tf
PA0763 154 tf
PA0764 154 tf
PA0961 154 tf
PA1099 154 tf
PA1850 154 tf
PA1998 154 tf
PA2047 154 tf
PA2622 154 tf
PA3604 154 tf
PA3622 154 tf
PA3714 154 tf
PA3815 154 tf
PA4354 154 tf
PA4581 154 tf
PA4890 154 tf
PA5253 154 tf
PA5261 154 tf
PA5274 154 tf
PA5337 154 tf
PA5483 154 tf
PA5511 154 tf

Warning: PA3692 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
3138 8.70e-02 Gct.GaAaAAA
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3139 3.20e+03 tTtCcgCtta
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3822 2.80e+01 aAGGAgtt
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3823 9.90e+01 GAA.aatggACCGgagGGcC
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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 PA3692

PA3692 is enriched for 3 functions in 3 categories.
Enrichment Table (3)
Function System
Outer membrane protein and related peptidoglycan-associated (lipo)proteins cog/ cog
cell outer membrane go/ cellular_component
integral to membrane go/ cellular_component
Module neighborhood information for PA3692

PA3692 has total of 18 gene neighbors in modules 154, 504
Gene neighbors (18)
Gene Common Name Description Module membership
PA0038 PA0038 hypothetical protein (NCBI) 279, 504
PA0460 PA0460 hypothetical protein (NCBI) 169, 504
PA0853 PA0853 probable oxidoreductase (NCBI) 107, 154
PA0854 fumC2 fumarate hydratase (NCBI) 107, 154
PA1323 PA1323 hypothetical protein (NCBI) 107, 154
PA1324 PA1324 hypothetical protein (NCBI) 154, 504
PA2754 PA2754 hypothetical protein (NCBI) 169, 504
PA2815 PA2815 probable acyl-CoA dehydrogenase (NCBI) 154, 233
PA3040 PA3040 hypothetical protein (NCBI) 154, 233
PA3041 PA3041 hypothetical protein (NCBI) 154, 504
PA3042 PA3042 hypothetical protein (NCBI) 154, 504
PA3691 PA3691 hypothetical protein (NCBI) 154, 504
PA3692 PA3692 probable outer membrane protein precursor (NCBI) 154, 504
PA4785 PA4785 acetyl-CoA acetyltransferase (NCBI) 322, 504
PA4876 osmE osmotically inducible lipoprotein OsmE (NCBI) 169, 504
PA4880 PA4880 probable bacterioferritin (NCBI) 107, 154
PA5060 phaF polyhydroxyalkanoate synthesis protein PhaF (NCBI) 154, 279
PA5212 PA5212 hypothetical protein (NCBI) 147, 504
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 PA3692
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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