171:. Comparable to bacterial growth curves, the respiration kinetic curves may provide valuable information coded in the length of the lag phase λ, the respiration rate μ (corresponding to the steepness of the slope), the maximum cell respiration A (corresponding to the maximum value recorded), and the area under the curve (AUC). In contrast to
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improving genome annotation. In contrast to many of the hitherto available molecular high-throughput technologies, phenotypic testing is processed with living cells, thus providing comprehensive information about the performance of entire cells. The major applications of the PM technology are in the fields of
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violet, which produces a purple color. The more rapid this metabolic flow, the more quickly purple color forms. The formation of purple color is a positive reaction. interpreted such that the sole carbon source is used as an energy source. A microplate reader and incubation facility are needed to
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technologies have made it possible to assay the expression level of thousands of genes or proteins all a once, phenotype microarrays (PMs) make it possible to quantitatively measure thousands of cellular phenotypes simultaneously. The approach also offers potential for testing gene function and
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data. Other software tools are PheMaDB, which provides a solution for storage, retrieval, and analysis of high throughput phenotype data, and the PMViewer software which focuses on graphical display but does not enable further statistical analysis. The latter is not publicly available.
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Galardini, M.; Mengoni, A.; Biondi, E.G.; Semeraro, R.; Florio, A.; Bazzicalupo, M.; Benedetti, A.; Mocali, S. (2013), "DuctApe: A suite for the analysis and correlation of genomic and OmniLog™ Phenotype
Microarray data",
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Boccuto, L.; Chen, C.-F.; Pittman, A.R.; Skinner, C.D.; McCartney, H.J.; Jones, K.; Bochner, B.R.; Stevenson, R.E.; Schwartz, C.E. (2013), "Decreased tryptophan metabolism in patients with autism spectrum disorders",
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The principal idea of retrieving information about the abilities of an organism and its special modes of action when making use of certain energy sources can be equivalently applied to other macro-nutrients such as
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Chang, W.; Sarver, K.; Higgs, B.; Read, T.; Nolan, N.; Chapman, C.; Bishop-Lilly, K.; Sozhamannan, S. (2011), "PheMaDB: A solution for storage, retrieval, and analysis of high throughput phenotype data",
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of cells to environmental challenges or exogenous compounds in a high-throughput manner. The phenotypic reactions are recorded as either end-point measurements or respiration kinetics similar to
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Vaas, L.A.I.; Sikorski, J.; Michael, V.; Göker, M.; Klenk, H.-P. (2012), "Visualization and curve-parameter estimation strategies for efficient exploration of
Phenotype MicroArray kinetics",
191:. "opm" contains tools for analyzing PM data including management, visualization and statistical analysis of PM data, covering curve-parameter estimation, dedicated and customizable plots,
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Omsland, A.; Cockrell, D.C.; Howe, D.; Fischer, E.R.; Virtaneva, K.; Sturdevant, D.E.; Porcella, S.F.; Heinzen, R.A. (2009), "Host cell-free growth of the Q fever bacterium
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provide the appropriate incubation conditions, and to automatically read the intensity of colour formation during tetrazolium reduction in intervals of, e.g., 15 minutes.
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Proprietary and commercially available software is available that provides a solution for storage, retrieval, and analysis of high throughput phenotype data. A powerful
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Vaas, L.A.I.; Sikorski, J.; Hofner, B.; Fiebig, A.; Buddruhs, N.; Klenk, H.-P.; Göker, M. (2013), "opm: An R Package for
Analysing OmniLog® Phenotype MicroArray Data",
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Vaas, L.A.I.; Marheine, M.; Sikorski, J.; Göker, M.; Schumacher, M. (2013), "Impacts of pr-10a overexpression at the molecular and the phenotypic level",
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Bochner, B.R.; Gadzinski, P.; Panomitros, E. (2001), "Phenotype MicroArrays for High
Throughput Phenotypic Testing and Assay of Gene Function",
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Hofner, B.; Boccuto, L.; Göker, M. (2015), "Controlling false discoveries in high-dimensional situations: Boosting with stability selection",
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Bochner, B.R.; Savageau, M.A. (1977), "Generalized indicator plate for genetic, metabolic, and taxonomic studies with microorganisms",
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can be measured in environmental conditions where cellular replication (growth) may not be possible, and that it is more accurate than
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During a positive reaction, the longitudinal kinetics are expected to appear as sigmoidal curves in analogy to typical bacterial
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to re-analyse autism PM data and detect more determining factors. The "opm" package has been developed and is maintained at the
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Montero-Calasanz, M.C.; Göker, M.; Pötter, G.; Rohde, M.; Spröer, C.; Schumann, P.; Klenk, A.A.; Gorbushina, H.-P. (2013), "
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Proceedings of the
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sp. nov., a novel actinomycete isolated from
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