Briefly, based on the expression differentiation between two samples, we compared the fold changes of KEGG gene set Si against the background expression changes denoted by G-Si, where G is the union of all KEGG gene sets.
To identify these age-specific changes responsible for the variation between the 4 and 6 months samples, we compared transcript profiles from all 4 months samples (4 AD and 4 WT, 8 in total) to profiles from all 6 months samples (4 AD and 3 WT, 7 in total) using Cuffdiff (see Methods).
We next quantified the pMad gradient in βPS − embryos (Umulis et al., 2010) To circumvent staining variability between samples, we only compared βPS − embryos to siblings that were maternal βPS − zygotic βPS+, as these embryos could be processed together throughout.
To assess the representativeness of the sample, we compared characteristics between the 736 not participating and the 110 participating physicians.
To compare CNV between samples, we calculated the significance of a difference using a t-test and p-value based on the normalized counts and normalized uncertainties.
To compare the germination rate between samples, we used an arcsin square root transformation of this variable.
To compare overall gene expression between the OP and CP samples, we first compared the genes expressed in each.
To detect sample tracking errors, we compared genotypes between all samples.
The differences of the percentages between samples were compared by paired two-tailed t test.
The differences of the levels between samples were compared using paired two-tailed t test.
