Table 3.

Comparisons between ds mRNAs identified by calculation and the genes corresponding to endo-siRNAs associated with Ago2 published from two different studies.

Study	nb of genes identified in the studies	nb of genes in our filtered list	Sensitivity	Specificity	p-value
Ghildiyal et al. S2	620	274	0.44	0.78	7.6x10−12
Ghildiyal et al. WT head	646	331	0.51	0.79	8.4x10−12
Czech et al. S2	95	51	0.54	0.76	2.2x10−10
Czech et al. ovaries	53	34	0.64	0.76	9.1x10−10
Total	1252	585	0.47	0.81	1.8x10−11

The numbers of genes corresponding to sequenced endo-siRNAs isolated by pull-down by Czech et al. [23] and Ghildiyal et al. [22] were retrieved according to the procedure described in the ‘Materials and Methods’ section. Briefly, all the reads in Ghildiyal et al.’s libraries were considered, and 50 reads for each sequence (as a cut-off) were retained for gene identification from Czech et al.’s libraries. The predictions are the numbers of these genes that are present in our calculated list of 4318 genes retaining only those showing the potential to form duplex RNAs with a minimum of 5 different other RNAs. The table displays the sensitivity values, corresponding to the number of computationally predicted genes found in the pull-down assays, along with the specificity values, corresponding to the number of genes that were not predicted to form a dsRNA and were not found in the pull-down assays. The p-values represent the probability of obtaining these results by chance.