Gene ontology (GO) term enrichment analysis showed that genes related to cell cycle (P = 9.85E−09), development (P = 1.2E−06), cell differentiation (P = 1.36E−06), cell proliferation (P = 2.53E−07), and lipid metabolism (P = 9.43E−04) are overrepresented in our dataset (ratios >twofold, Table 1).
The genes PGRP-SC2, which is important in dampening the immune response [33], was one of the few genes to be down-regulated in both our male and female datasets (females: ratio infected/uninfected = 0.67, P = 0.005; males: ratio = 0.81, P = 0.015).
In both train and test datasets the ratio between the positive and negative data samples are maintained as 1 5.
When comparing multiple datasets, the Ratio filtering test must be satisfied in all datasets for a given gene to be selected.
The number of probes that are found in the original data, but not in the average permuted dataset is an estimation of the amount of truly aging-associated genes [ 10], therefore from the dataset permutation analysis we can conclude that in the significantly age-regulated datasets the ratio signal to noise is very small.
Although the ratios were nearly constant in the claims dataset, the ratio increased over time in the FAERS dataset; that is, the monthly AE rate for the branded levetiracetam product, was on average almost 10 times that of the generic products toward the end of the study period.
Based on the LOWESS regression of this large comparison dataset, 3′:5′ ratio threshold criteria equivalent to RIN cut-off values can be proposed for the selection of RNA samples for RT-qPCR analyses.
In our dataset, the ratio between the intensity of the bands at 1430 and 900 cm−1 for the initial cellulose, the hydrolyzed cellulose, and the sonicated cellulose was 1.74, 1.82, and 1.86, respectively.
In our dataset, the ratio of nonsynonymous-synonymous positions in the coding region was about 1∶2.02 (Figure 2); this ratio fits very well with the proportion of 1∶1.97 that was obtained previously [53] in a survey of >5100 entire genomes (see caveats in [56]).
In this dataset, the ratio of damaging to neutral mutations was 6 1.
For each dataset, likelihood ratio tests (LRT) for detection of positive selection were examined using M7-M8 and M8a-M8 comparisons.
