Enrichment was determined using the total set of all detected proteins as the background set, and using the following settings: Similarity Term Overlap: 4; Similarity Threshold: 0.35; Initial Group Membership: 4; Final Group Membership: 4; Multiple Linkage Threshold: 0.50.
For both strategies we used the total set of RTSSs in all metaclusters as background data.
Thus, using the total set under this proportionality assumption, the percentage of chimeric TE insertions detected relative to expectation is little changed (65 out of 341, 19%).
For the co-expression analysis, we calculated the mean value of each gene for a given species using the total set of the arrays used to assay that species.
We thus made the analysis using the total set of genes expressed in each male or female cone of the gymnosperms, independently of its expression in the other, female or male, cone.
Using the total set of 22 fresh-frozen HCC tissues (Table S2 in Additional file 1), the CpG sites in SLC22A1 with the strongest inverse correlation with mRNA expression in HCC (Table 1) were remarkably located upstream of the translational start site in exon 1.
Finally, by using the total reference set, the average PR' and SD are 0.96 and 0.18, respectively.
The duplicate samples were averaged, then the value was determined for each gene for each donor using the total gene set average as the calibrator.
It should be noted that in these cases, unlike the original 3 retinal samples, the validation rate was determined by using the total capture set as reference, rather than the individual transcriptome as a reference.
We used the total sample set, 78 loci (under HWE) and K = 1 8, Bayesian analysis of population structure generated a maximum probability of the data with K = 7, but the modal value of Δ K was at K = 3 (fig. 3).
