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In total, 7000 ~ 54000 peaks were called using a stringent peak detection threshold p-value of p < 10−5 (Additional file 2: Table S2).
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Using a stringent peak-calling algorithm and validating its results by ChIP-PCR, we identified 28 major KAP1-enriched regions on the HCMV genome.
Using a stringent threshold (a promoter array peak signal >2.0, compared to the input DNA signal) and a false discovery rate of <0.05, we found that Sox2 was bound to the promoter regions of 1,830 genes in RU cells and 456 genes in RR cells, with an overlap of only 62 genes between the two cell subsets (illustrated in Figure 1A).
Sites with significant Pfh1 occupancy were identified with the Model-based Analysis of ChIP-seq peak calling software (MACS; Zhang et al. [ 49]), using a stringent cutoff for both ChIP and input DNA (P <10-5).
The identification of CNV regions (CNVRs) was performed by using a stringent procedure.
We report these results using a stringent family-wise error (FWE) volume-corrected threshold of P<0.05.
ClCE8 homologs were retrieved from the NCBInr protein database using a stringent E value of 1e-50.
The hit rate using a stringent cutoff of 2-fold inhibition (activity of <0.5) was 0.05%.
Using a stringent filtering method, we identified 3.1 million SNPs, 193 thousand INDELs, and 282 CNVs.
The gene expression differences of the categories were determined using a stringent default value.
On the other hand, HMM_RA is evaluated using a stringent ten-fold cross-validation.
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