Table 1 Summary of piRNA cluster identification methods and results from previous studies
From: proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis
study | organism | identified clusters | criteria for detection of clusters |
|---|---|---|---|
Aravin et al. 2006 [3] | human/mouse | 14/42 | at least 4 piRNA loci per cluster, maximum distance between two piRNA loci 15 kb |
Girard et al. 2006 [4] | human/mouse/rat | 186/123/157 | at least 5 piRNA loci/5kb, at least 10 piRNA loci per cluster, only sequence reads that mapped 1-5 times to the genome were considered, sequence reads mapped to genome allowing up to 2 mismatches |
Lau et al. 2006 [5] | mouse/rat | 94/100 | at least 20 single-copy loci, at least 1 piRNA locus/kb |
Lakshmi and Agrawal 2007 [7] | human/mouse/rat | 114/2710/189 | at least n** single-copy loci/20kb, at least 2 piRNA loci/kb |
Grivna et al. 2006 [12] | mouse | 35 | * |
Watanabe et al. 2006 [13] | mouse | 34 | p < = 0.05, where p = (s/S)n-1×NCn S: genome size (bp), s: cluster size (bp), N: total number of sequence hits, n: number of hits in cluster |