Phenotype-defining parameters were used as dependent variables, rat strain as a fixed factor, and mean centroids of the most significant gene subsets (derived from GSEA analyses) as the independent explanatory covariates.
Upon sub-division of patients into ER+ and ER− cohorts, this correlation was most significant in the subset of ER+ breast cancer cases (Fig 4), supporting our initial findings that the SPINK1 transcript displayed positive association with poor prognosis predominantly with ER+ cases.
The power of the AML test has been found to be similar to or better than all other tests (rank truncated product, unrestricted maximum likelihood, restricted space maximum likelihood, most significant SNP, Global χ2, Best subset χ2) across a wide range of scenarios for the alternative hypothesis [31].
For the most significant linkage results from the subset analyses, the FLexible Ordered SubSet (FLOSS v1.4.1, http://www.stat.auckland.ac.nz/∼browning/floss/floss.htm osa) software was used to generate empirical p values (47).
Within the NHB subset, the most significant genes were UNC13C and DSCAM.
Within the NHW subset, the most significant genes were TBC1D2, SDC2 and PCDH7.
Table S4: Fifty most significant f3 statistics for the subset of 13 populations used in Treemix analysis.
The thinning process generates subsets of "most significant" points, such that the piecewise linear interpolants over the Delaunay triangulations of these subsets approximate progressively the function values sampled at the original scattered points, and such that the approximation errors are small relative to the number of points in the subsets.
While we saw an overall increase in the number of monocytes in all three subsets in the elderly, the most significant increase occurs in the non-classical subset (Fig. 8b), consistent with the concept that senescent cells accumulate with age.
