eigenarray meaning: definition, etymology

eigenarray

noun

Etymology From eigen- + array.

Biology, Genetics, Medicine, Natural sciences, Sciences (mathematics) One of a set of left singular vectors of a genes x samples matrix that tabulates, e.g., the mRNA or gene expression of the genes across the samples, where the samples were assayed by using DNA microarrays. The corresponding right singular vector is the corresponding eigengene.

1999, O. Alter et al., ‘‘Singular Value Decomposition for Gene Expression Data Processing and Modeling.’’ In: After the Genome V (December 6–10, 1999, Jackson Hole, WY). We describe the use of singular value decomposition in transforming gene expression data from genes/arrays space to ‘‘eigengenes’’/‘‘eigenarrays’’ space, where the eigengenes and eigenarrays are unique orthonormal superpositions of the genes and arrays, respectively.
2000, O. Alter et al., ‘‘Singular value decomposition for genome-wide expression data processing and modeling,’’ Proc. Natl. Acad. Sci. USA 97 (18), pp. 10101–10106. doi:10.1073/pnas.97.18.10101. After normalization and sorting, the significant eigengenes and eigenarrays can be associated with observed genome-wide effects of regulators, or with measured samples, in which these regulators are overactive or underactive, respectively.

4 more examples

2002, T. O. Nielsen et al., ‘‘Molecular Characterisation of Soft Tissue Tumours: a Gene Expression Study,’’ Lancet 359 (9314), pp. 1301–1307. doi: 10.1016/S0140-6736(02)08270-3. The separation of the calponin-positive leiomyosarcoma subgroup from the calponin-negative tumours was dominant, and resulted in an important eigengene and corresponding eigenarray.
2006, C. M. Li and R. R. Klevecz, ‘‘A rapid genome-scale response of the transcriptional oscillator to perturbation reveals a period-doubling path to phenotypic change,’’ Proc. Natl. Acad. Sci. USA 103 (44), pp. 16254–16259. doi: 10.1073/pnas.0604860103. A reconstruction of the attractor can be seen in the plot of the principal eigengenes 2, 3, and 4.
2008, A. Y. Gracey et al., ‘‘Rhythms of Gene Expression in a Fluctuating Intertidal Environment,’’ Curr. Biol. 18 (19), pp. 1501-1507. doi: 10.1016/j.cub.2008.08.049. Significantly correlated with the first eigengene were GO terms that we classified as being broadly associated with ‘‘metabolism’’ because this cluster was enriched for genes involved in the tricarboxylic acid cycle (TCA), the electron transport chain, metabolism, ATP synthesis, and protein degradation.
2012, M. J. Hawrylycz et al., ‘‘An anatomically comprehensive atlas of the adult human brain transcriptome,’’ Nature 489 (7416), pp. 391–399. doi: 10.1038/nature11405. Each module is represented by an ‘eigengene’ corresponding to its expression pattern across structures (first left singular vector of the gene × structure matrix), and genes highly correlated with the module eigengene are called ‘hub’ genes.

Related terms: eigengenome