Organism : Pseudomonas aeruginosa | Module List :
probable phenazine biosynthesis protein (NCBI)
Functional Annotations (1)
|antibiotic biosynthetic process||go/ biological_process|
Regulation information for PA4210(Mouseover regulator name to see its description)
Motif information (de novo identified motifs for modules)
There are 4 motifs predicted.
|Motif Id||e-value||Consensus||Motif Logo|
Functional Enrichment for PA4210
|antibiotic biosynthetic process||go/ biological_process|
Module neighborhood information for PA4210
|Gene||Common Name||Description||Module membership|
|PA0051||phzH||potential phenazine-modifying enzyme (NCBI)||152, 292|
|PA0140||ahpF||alkyl hydroperoxide reductase subunit F (NCBI)||152, 224|
|PA0534||PA0534||hypothetical protein (NCBI)||152, 212|
|PA0535||PA0535||probable transcriptional regulator (NCBI)||152, 212|
|PA0848||PA0848||probable alkyl hydroperoxide reductase (NCBI)||152, 550|
|PA0849||trxB2||thioredoxin reductase 2 (NCBI)||152, 187|
|PA1901||phzC2||phenazine biosynthesis protein PhzC (NCBI)||250, 356|
|PA1902||phzD2||phenazine biosynthesis protein PhzD (NCBI)||250, 356|
|PA1903||phzE2||phenazine biosynthesis protein PhzE (NCBI)||250, 356|
|PA1904||phzF2||probable phenazine biosynthesis protein (NCBI)||250, 356|
|PA1905||phzG2||probable pyridoxamine 5'-phosphate oxidase (NCBI)||250, 356|
|PA1927||metE||5-methyltetrahydropteroyltriglutamate-- homocysteine methyltransferase (NCBI)||152, 236|
|PA2193||hcnA||hydrogen cyanide synthase HcnA (NCBI)||250, 356|
|PA2194||hcnB||hydrogen cyanide synthase HcnB (NCBI)||250, 356|
|PA2195||hcnC||hydrogen cyanide synthase HcnC (NCBI)||250, 356|
|PA2274||PA2274||hypothetical protein (NCBI)||152, 309|
|PA2698||PA2698||probable hydrolase (NCBI)||152, 268|
|PA2794||PA2794||hypothetical protein (NCBI)||152, 188|
|PA2795||PA2795||hypothetical protein (NCBI)||152, 326|
|PA3237||PA3237||hypothetical protein (NCBI)||152, 538|
|PA3287||PA3287||hypothetical protein (NCBI)||152, 432|
|PA3600||PA3600||hypothetical protein (NCBI)||152, 361|
|PA3601||PA3601||hypothetical protein (NCBI)||152, 361|
|PA4129||PA4129||hypothetical protein (NCBI)||46, 250|
|PA4130||PA4130||probable sulfite or nitrite reductase (NCBI)||46, 250|
|PA4131||PA4131||probable iron-sulfur protein (NCBI)||46, 250|
|PA4132||PA4132||hypothetical protein (NCBI)||46, 250|
|PA4133||PA4133||cytochrome c oxidase subunit (cbb3-type) (NCBI)||46, 250|
|PA4134||PA4134||hypothetical protein (NCBI)||46, 250|
|PA4205||mexG||hypothetical protein (NCBI)||152, 309|
|PA4206||mexH||probable Resistance-Nodulation-Cell Division (RND) efflux membrane fusion protein precursor (NCBI)||152, 309|
|PA4207||mexI||probable Resistance-Nodulation-Cell Division (RND) efflux transporter (NCBI)||152, 309|
|PA4208||opmD||probable outer membrane protein precursor (NCBI)||152, 309|
|PA4209||phzM||probable phenazine-specific methyltransferase (NCBI)||112, 250|
|PA4210||phzA1||probable phenazine biosynthesis protein (NCBI)||152, 250|
|PA4211||phzB1||probable phenazine biosynthesis protein (NCBI)||250, 356|
|PA4217||phzS||flavin-containing monooxygenase (NCBI)||250, 356|
|PA4612||PA4612||hypothetical protein (NCBI)||152, 344|
|PA4613||katB||catalase (NCBI)||152, 313|
|PA4623||PA4623||hypothetical protein (NCBI)||108, 152|
|PA4881||PA4881||hypothetical protein (NCBI)||108, 152|
|PA5180||PA5180||hypothetical protein (NCBI)||152, 425|
|PA5181||PA5181||probable oxidoreductase (NCBI)||152, 425|
Gene Page Help
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.
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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".
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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.
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.
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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.
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CircVisOur 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.
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