Table 3 Numbers of significant distal HVRs identified by applying different parameter estimation methods with various cutoffs of the BH-adjusted p-value
From: HyperChIP: identification of hypervariable signals across ChIP-seq or ATAC-seq samples
Parameter estimation | Data set | Number of significant distal HVRs | ||
|---|---|---|---|---|
0.01 | 0.05 | 0.1 | ||
Original | H3K27ac ChIP-seq | 2 | 8 | 12 |
ATAC-seq | 0 | 3 | 4 | |
Pol II ChIP-seq | 0 | 0 | 0 | |
Lower 10% + winsorization | H3K27ac ChIP-seq | 289 | 1372 | 2621 |
ATAC-seq | 3124 | 6830 | 10,234 | |
Pol II ChIP-seq | 602 | 1400 | 2122 | |