Phenotype microarray

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Technology for phenotyping of cells

title: "Phenotype microarray" type: doc version: 1 created: 2026-02-28 author: "Wikipedia contributors" status: active scope: public tags: ["microbiology", "physiology", "phenomics"] description: "Technology for phenotyping of cells" topic_path: "science/biology" source: "https://en.wikipedia.org/wiki/Phenotype_microarray" license: "CC BY-SA 4.0" wikipedia_page_id: 0 wikipedia_revision_id: 0

::summary Technology for phenotyping of cells ::

The phenotype microarray approach is a technology for high-throughput phenotyping of cells. A phenotype microarray system enables one to monitor simultaneously the phenotypic reaction 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 growth curves.

Usages

High-throughput phenotypic testing is increasingly important for exploring the biology of bacteria, fungi, yeasts, and animal cell lines such as human cancer cells. Just as DNA microarrays and proteomic 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.{{Citation | last = Bochner | first = B.R. | title = Global phenotypic characterization of bacteria | journal = FEMS Microbiology Reviews | volume = 33 | pages = 191–205 | year = 2009 | doi = 10.1111/j.1574-6976.2008.00149.x | pmid = 19054113 | issue = 1 | pmc = 2704929 | last1 = Bochner | first1 = B.R. | last2 = Gadzinski | first2 = P. | last3 = Panomitros | first3 = E. | title = Phenotype MicroArrays for High Throughput Phenotypic Testing and Assay of Gene Function | journal = Genome Research | volume = 11 | pages = 1246–1255 | year = 2001 | doi = 10.1101/gr.186501 | issue = 7 | pmid = 11435407 | pmc = 311101 | last1 = Montero-Calasanz | first1 = M.C. | last2 = Göker | first2 = M. | last3 = Pötter | first3 = G. | last4 = Rohde | first4 = M. | last5 = Spröer | first5 = C. | last6 = Schumann | first6 = P. | last7 = Klenk | first7 = A.A. | last8 = Gorbushina | first8 = H.-P. | title = Geodermatophilus telluris sp. nov., a novel actinomycete isolated from Saharan desert sand in Chad | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 13 | issue = Pt 6 | pages = 2254–2259 | year = 2013 | doi = 10.1099/ijs.0.046888-0 | pmid = 23159748 | hdl = 10033/299082 | hdl-access = free | last1 = Boccuto | first1 = L. | last2 = Chen | first2 = C.-F. | last3 = Pittman | first3 = A.R. | last4 = Skinner | first4 = C.D. | last5 = McCartney | first5 = H.J. | last6 = Jones | first6 = K. | last7 = Bochner | first7 = B.R. | last8 = Stevenson | first8 = R.E. | last9 = Schwartz | first9 = C.E. | title = Decreased tryptophan metabolism in patients with autism spectrum disorders | journal = Molecular Autism | volume = 4 | year = 2013 | doi = 10.1186/2040-2392-4-16 | pmid = 23731516 | issue = 16 | page = 16

Technology

A sole carbon source that can be transported into a cell and metabolized to produce NADH engenders a redox potential and flow of electrons to reduce a tetrazolium dye,{{Citation | last1 = Bochner | first1 = B.R. | last2 = Savageau | first2 = M.A. | title = Generalized indicator plate for genetic, metabolic, and taxonomic studies with microorganisms | journal = Applied and Environmental Microbiology | volume = 33 | pages = 434–444 | year = 1977 | pmid = 322611 | issue = 2 | doi = 10.1128/AEM.33.2.434-444.1977 | pmc = 170700 | bibcode = 1977ApEnM..33..434B

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 nitrogen, sulfur, or phosphorus and their compounds and derivatives. As an extension, the impact of auxotrophic supplements or antibiotics, heavy metals or other inhibitory compounds on the respiration behaviour of the cells can be determined.

Data structure

During a positive reaction, the longitudinal kinetics are expected to appear as sigmoidal curves in analogy to typical bacterial growth curves. 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 bacterial growth curves, there is typically no death phase in PMs, as the reduced tetrazolium dye is insoluble.

Software

Proprietary and commercially available software is available that provides a solution for storage, retrieval, and analysis of high throughput phenotype data. A powerful free and open source software is the "opm" package based on R.{{Citation | last1 = Vaas | first1 = L.A.I. | last2 = Sikorski | first2 = J. | last3 = Michael | first3 = V. | last4 = Göker | first4 = M. | last5 = Klenk | first5 = H.-P. | title = Visualization and curve-parameter estimation strategies for efficient exploration of Phenotype MicroArray kinetics | journal = PLOS ONE | volume = 7 | article-number = e34846 | year = 2012 | doi = 10.1371/journal.pone.0034846 | issue = 4 | pmid = 22536335 | pmc = 3334903 | bibcode = 2012PLoSO...734846V | doi-access = free | last1 = Vaas | first1 = L.A.I. | last2 = Sikorski | first2 = J. | last3 = Hofner | first3 = B. | last4 = Fiebig | first4 = A. | last5 = Buddruhs | first5 = N. | last6 = Klenk | first6 = H.-P. | last7 = Göker | first7 = M. | title = opm: An R Package for Analysing OmniLog® Phenotype MicroArray Data | journal = Bioinformatics | year = 2013 | doi = 10.1093/bioinformatics/btt291 | volume = 29 | issue = 14 | pages = 1823–4 | pmid = 23740744 | doi-access = free Citation | last1 = Hofner | first1 = B. | last2 = Boccuto | first2 = L. | last3 = Göker | first3 = M. | title = Controlling false discoveries in high-dimensional situations: Boosting with stability selection | journal = BMC Bioinformatics | year = 2015 | doi = 10.1186/s12859-015-0575-3 | volume = 16 | page = 144 | pmid = 25943565 | pmc=4464883 | doi-access = free | last1 = Galardini | first1 = M. | last2 = Mengoni | first2 = A. | last3 = Biondi | first3 = E.G. | last4 = Semeraro | first4 = R. | last5 = Florio | first5 = A. | last6 = Bazzicalupo | first6 = M. | last7 = Benedetti | first7 = A. | last8 = Mocali | first8 = S. | title = DuctApe: A suite for the analysis and correlation of genomic and OmniLog™ Phenotype Microarray data | journal = Genomics | volume = 103 | issue = 1 | pages = 1–10 | year = 2013 | doi = 10.1016/j.ygeno.2013.11.005 | pmid = 24316132 | doi-access = free | arxiv = 1307.4276 | last1 = Chang | first1 = W. | last2 = Sarver | first2 = K. | last3 = Higgs | first3 = B. | last4 = Read | first4 = T. | last5 = Nolan | first5 = N. | last6 = Chapman | first6 = C. | last7 = Bishop-Lilly | first7 = K. | last8 = Sozhamannan | first8 = S. | title = PheMaDB: A solution for storage, retrieval, and analysis of high throughput phenotype data | journal = BMC Bioinformatics | volume = 12 | page = 109 | year = 2011 | doi = 10.1186/1471-2105-12-109 | pmid = 21507258 | pmc = 3097161 | doi-access = free | last1 = Borglin | first1 = S. | last2 = Joyner | first2 = D. | last3 = Jacobsen | first3 = J. | last4 = Mukhopadhyay | first4 = A. | last5 = Hazen | first5 =T.C. | title = Overcoming the anaerobic hurdle in phenotypic microarrays: Generation and visualization of growth curve data for Desulfovibrio vulgaris Hildenborough | journal = Journal of Microbiological Methods | volume = 76 | pages = 159–168 | year = 2009 | doi = 10.1016/j.mimet.2008.10.003 | pmid = 18996155 | issue = 2 | url = https://digital.library.unt.edu/ark:/67531/metadc929160/m2/1/high_res_d/953769.pdf

References

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