In order to reduce the number of false positive predictions we considered only targets predicted by both algorithms, which resulted in about 110.000 miRNA-mRNA pairs.
Liver parenchymal cells themselves, in contrast to mononuclears like Kupffer cells, are generally considered only targets but not producers of these important mediators.
To determine putative mRNA targets for these candidates, we used six different computational target prediction tools and considered only targets that were predicted by at least two target prediction algorithms.
We opted to consider only targets that were commonly predicted by at least 5 out of the 7 prediction databases, and obtained a list of 5,806 putative target genes (Fig. 4a).
They were: Considering only targets who were newcomers, categorization scores for the male/female distinction were significantly greater than zero (M = 0.99, SD = 1.30, t54 = 5.64, one-tailed p < 0.001, r = 0.61).
Considering only targets who were veterans, categorization scores for the male/female distinction were also significantly greater than zero (M = 0.39, SD = 1.40, t54 = 2.07, one-tailed p = 0.022, r = 0.27).
Indeed they were: Considering only targets who were newcomers, categorization scores for the free rider/cooperator distinction were significantly greater than zero (M = 0.52, SD = 1.57, t64 = 2.64, one-tailed p = 0.005, r = 0.31).
They were not: Considering only targets who were free riders, the categorization score for tenure was not significantly greater than zero (M = 0.05, SD = 1.67, t64 = 0.26, one-tailed p = 0.398, r = 0.03).
Considering only targets who were veterans, categorization scores for the free rider/cooperator distinction were also significantly greater than zero (M = 0.58, SD = 1.50, t64 = 3.11, one-tailed p = 0.001, r = 0.36).
We considered only sRNA-target pairs with a score smaller or equal to 4. Three categories of cleavage profiles are defined by Addo-quaye et, al. [41].
