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Because of the expected overlap in the patterns of gene expression in the glomerulus gene set with the normal cortex, we focused our analysis on the cortex gene set.
Regarding the first issue, parent-offspring conflict over mate choice in contemporary Western populations has been found to contain considerable conflict of interest, as well as some expected overlap, in preferred attributes [28] [31].
These studies did not, however, investigate the expected overlap in cortical activation due to the stimulation of different fingers.
With low power, the expected overlap in sites predicted to be under selection would also be low [ 19].
Model-based methods may conform better with the expected overlap in biological cell subpopulations, but do not normally scale well to very large datasets, and have a high computational load.
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The differential genomic feature overlap analyses of eQTMs were done by comparing the number of observed overlaps for positive and negative eQTMs, with the number of expected overlaps in non-eQTM sites.
However, we expect overlap in the description of chemical structure by various groups of descriptors.
When we take the top 500 genes with increased variability in U-CLL in each dataset (see Additional file 1), we find a significantly higher than expected overlap (69 genes in both lists, Hypergeometric test, P value <2.2e-16 <2.2e-16
To score k-mers, the expected overlap for co-occurrence in syntenic pairs were calculated from single genome frequencies.
Second, of the 28 Mec1/Tel1-dependent and Rad53-independent phosphoproteins that were induced after exposure of wildtype and rad53Δ yeast to methyl methanosulfonate, 7 were present in our list (expected overlap of 1.787 proteins, p = 2.575e-04) [ 12].
For example, the number of genes activated by both Pou5f1 and Sox2 (N = 137, Fig. 5B) was significantly higher than expected from permutation of 1729 genes with strong binding sites (with SPF > 95-percentile in control genes); expected overlap was only 43.61 genes (chi-square = 50.95, p < 0.001).
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