To learn possible similarities and differences in gene activities affected by drought between reproductive and other tissues, we compared our results with other transcriptomes from vegetative tissues.
When comparing transcriptional fingerprints between tissues, we observed that sDCs were enriched for metabolic pathways, while vDCs were enriched for immune-related networks.
The previous report [ 18] compared DNAs between testis and other tissues, whereas we compared cfsDNA between vasectomized men and healthy donors.
To determine the background level of similarity between unrelated individuals, we compared the same tissue between 79 different random pairs of unrelated subjects.
Relative expression between tissues was compared by a one-way ANOVA on log transformed data followed by a post hoc Tukey test.
When between tissues were compared, 57 and 78 miRNAs were differentially expressed at infected and non-infected states, respectively (Tables 5, 6).
Genome-wide levels of DNA methylation vary between tissues, and compared with other tissues, the placenta has been reported to demonstrate a global decrease in methylation as well as decreased methylation of X-linked promoters.
To capture this potential effect of LTRs, we compared the correlation between tissues calculated from the LTR-associated genes (LTR+), and the correlation between tissues calculated from LTR-absent genes (LTR−).
In order to verify this hypothesis, we compared the tissue specificity between the ubiquitously expressed genes (expression breadth ≥ 14) and the intermediately expressed genes (expression breadth = 8 or 9) with similar expression level.
Systematic use of integrated gene expression data, such as GeneSapiens, allows the definition of universal cutoff points for transcriptional activity across all tissue types, which then makes it possible to identify active gene expression regulation in a tissue even when the relative expression increase between tissues to be compared is only modest.
