Organism : Pseudomonas aeruginosa | Module List :
probable hemagglutinin (NCBI)
Functional Annotations (2)
Regulation information for PA0041(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 PA0041
Module neighborhood information for PA0041
|Gene||Common Name||Description||Module membership|
|PA0011||PA0011||lipid A biosynthesis lauroyl acyltransferase (NCBI)||62, 86|
|PA0041||PA0041||probable hemagglutinin (NCBI)||62, 337|
|PA0048||PA0048||probable transcriptional regulator (NCBI)||62, 187|
|PA0054||PA0054||RNA 2'-phosphotransferase (NCBI)||20, 337|
|PA0193||PA0193||hypothetical protein (NCBI)||337, 425|
|PA0272||PA0272||probable transcriptional regulator (NCBI)||337, 537|
|PA0292||aguA||agmatine deiminase (NCBI)||62, 263|
|PA0322||PA0322||probable transporter (NCBI)||267, 337|
|PA0504||bioD||dithiobiotin synthetase (NCBI)||62, 253|
|PA0564||PA0564||probable transcriptional regulator (NCBI)||333, 337|
|PA0571||PA0571||hypothetical protein (NCBI)||62, 295|
|PA0606||PA0606||probable permease of ABC transporter (NCBI)||234, 337|
|PA0659||PA0659||hypothetical protein (NCBI)||62, 76|
|PA1051||PA1051||probable transporter (NCBI)||240, 337|
|PA1052||PA1052||hypothetical protein (NCBI)||240, 337|
|PA1068||PA1068||probable heat shock protein (hsp90 family) (NCBI)||62, 487|
|PA1149||PA1149||hypothetical protein (NCBI)||62, 355|
|PA1222||PA1222||probable membrane-bound lytic murein transglycolase A (NCBI)||62, 229|
|PA1229||PA1229||probable transcriptional regulator (NCBI)||71, 337|
|PA1233||PA1233||hypothetical protein (NCBI)||71, 337|
|PA1469||PA1469||hypothetical protein (NCBI)||245, 337|
|PA1504||PA1504||probable transcriptional regulator (NCBI)||62, 78|
|PA1526||PA1526||probable transcriptional regulator (NCBI)||62, 522|
|PA1726||bglX||periplasmic beta-glucosidase (NCBI)||49, 62|
|PA2267||PA2267||probable transcriptional regulator (NCBI)||62, 519|
|PA2289||PA2289||hypothetical protein (NCBI)||39, 62|
|PA2382||lldA||L-lactate dehydrogenase (NCBI)||62, 290|
|PA2455||PA2455||hypothetical protein (NCBI)||62, 363|
|PA2457||PA2457||hypothetical protein (NCBI)||62, 206|
|PA2462||PA2462||hypothetical protein (NCBI)||62, 297|
|PA2712||PA2712||hypothetical protein (NCBI)||245, 337|
|PA2720||PA2720||hypothetical protein (NCBI)||306, 337|
|PA2962||tmk||thymidylate kinase (NCBI)||1, 62|
|PA3020||PA3020||probable soluble lytic transglycosylase (NCBI)||62, 522|
|PA3078||PA3078||probable two-component sensor (NCBI)||20, 337|
|PA3086||PA3086||hypothetical protein (NCBI)||62, 387|
|PA3402||PA3402||hypothetical protein (NCBI)||337, 387|
|PA3627||ispF||2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (NCBI)||62, 139|
|PA3660||PA3660||probable sodium/hydrogen antiporter (NCBI)||20, 337|
|PA3661||PA3661||hypothetical protein (NCBI)||291, 337|
|PA3749||PA3749||probable major facilitator superfamily (MFS) transporter (NCBI)||175, 337|
|PA3777||xseA||exodeoxyribonuclease VII large subunit (NCBI)||62, 528|
|PA3778||PA3778||probable transcriptional regulator (NCBI)||62, 528|
|PA3884||PA3884||hypothetical protein (NCBI)||20, 337|
|PA4056||ribD||riboflavin-specific deaminase/reductase (NCBI)||62, 228|
|PA4092||hpaC||4-hydroxyphenylacetate 3-monooxygenase small chain (NCBI)||192, 337|
|PA4331||PA4331||hypothetical protein (NCBI)||62, 443|
|PA4332||PA4332||hypothetical protein (NCBI)||62, 443|
|PA4354||PA4354||hypothetical protein (NCBI)||108, 337|
|PA4356||xenB||xenobiotic reductase (NCBI)||62, 108|
|PA4376||pncB2||nicotinate phosphoribosyltransferase (NCBI)||337, 384|
|PA4393||PA4393||probable permease (NCBI)||20, 62|
|PA4488||PA4488||hypothetical protein (NCBI)||62, 66|
|PA4721||PA4721||sugar fermentation stimulation protein (NCBI)||53, 62|
|PA4779||PA4779||hypothetical protein (NCBI)||313, 337|
|PA4802||PA4802||hypothetical protein (NCBI)||337, 445|
|PA4807||selB||selenocysteine-specific elongation factor (NCBI)||49, 62|
|PA4893||ureG||urease accessory protein UreG (NCBI)||337, 380|
|PA4894||PA4894||hypothetical protein (NCBI)||337, 380|
|PA5014||glnE||glutamate-ammonia-ligase adenylyltransferase (NCBI)||3, 62|
|PA5035||gltD||glutamate synthase small chain (NCBI)||62, 189|
|PA5036||gltB||glutamate synthase large chain precursor (NCBI)||62, 451|
|PA5082||PA5082||probable binding protein component of ABC transporter (NCBI)||62, 74|
|PA5102||PA5102||hypothetical protein (NCBI)||337, 538|
|PA5280||sss||site-specific recombinase Sss (NCBI)||49, 62|
|PA5324||PA5324||probable transcriptional regulator (NCBI)||30, 337|
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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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.
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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.
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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.
- 2. Source gene
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