Table 1 Comparison of global trends of LoDEI and the Alu editing index

From: LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data

Dataset

AEI condition

AEI control

AEI difference

Adjusted p-value

LoDEI #+

LoDEI #−

ADAR1 KD

0.31 (2)

1.48 (2)

−1.17 [−1.20, −1.14]

0.0006

0

1624

sncRNA7SL OE

1.00 (5)

1.06 (5)

−0.06 [−0.07, −0.05]

0.00006

0

64

RO60 KO

1.16 (3)

1.07 (2)

0.09 [−0.06, 0.22]

0.46

114

0

MYCN-amp

1.13 (4)

0.95 (4)

0.18 [0.03, 0.36]

0.14

217

0

  1. Columns 1 and 2 show the mean of the AEI values of all samples of a set for all four datasets and the number of RNA-seq samples (n) per set. Column 3 shows the difference between the mean AEI values of columns 1 and 2 and the corresponding 95% confidence interval, and column 4 shows the Benjamini–Hochberg corrected two-sided t-test derived p values for the comparisons of the AEI means. Columns 5 and 6 show the number of detected windows by LoDEI with q values ≤0.1 with increased (#+) and decreased (#−) A-to-I signal. The column ’condition’ refers to the ADAR1 KD, sncRNA7SL OE, RO60 KO, and MYCN-amp samples.
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