Expression profile and identification of DEGs between patients
with ATA and those with AERD
From the 10 asthmatic patients collected, the average 35,160,551 pairs
of RNA-seq per sample was produced, and 35,115,725 pairs (7,039,115,605
bp) were presented after the adapter and low quality trimming (Table
S1). Gene expression profiling was conducted by reads mapping against
the human reference genome (hg19), and the normalization and sample
clustering was attempted to compare between the AERD and ATA groups
(Figure 1A and Table S2).
DEGs were selected according to aspirin intolerance, adjusting with
atopy status. Under the criteria of P value < 0.05 and
logFC ≥ |1|; we found 1,736 DEGs: 832 were
up-regulated and 904 were down-regulated in patients with AERD (Figure
1, B and C).
Estimation of methylation levels and D ifferentiallyM ethylated R egions (DMRs)
The number of statistically significant CpGs from the chip was 865,912
at the P value < 0.01 and 865,917 at the P value
< 0.05. Of the total samples (10 patients), CpG sites whose
uncertain methylation values were greater than 25% in the sum of NA,
and P values > 0.05 were excluded from further
analysis. The remaining 865,384 CpGs after the filtering were used for
subsequent analysis.
The DNA methylation profile was generated in 10 asthmatics. After
adjusting for atopy status, we found 1,401 DMPs using ChAMP (R-package
for methylation analysis pipeline): 13 with higher methylation and 1,388
with lower methylation in patients with AERD (Figure 2A and Table S3).
As shown above, the genomic distribution of extracted DMPs was confirmed
at the significance level of P value and the condition of aspirin
intolerance. Most DMPs from AERD and ATA were frequently observed at the
upstream regulatory region, such as TSS, UTR, and 1st Exon, according to
the ratio of the region occupied by whole genome (Figure 2B), suggesting
that methylation changes occur primarily in the regulatory domain.