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Fig. 7 | Genome Biology

Fig. 7

From: Tools and best practices for data processing in allelic expression analysis

Fig. 7

QC measures improve the power to detect biologically relevant AE at genes that have eQTLs (eGenes), where individuals that are heterozygous for the top eQTL SNP (eSNP) are expected to have more AE than homozygous individuals. Plot of median AE in heterozygous versus homozygous individuals for each eGene, before (a) and after (b) QC measures. Red points indicate a significant (1 % FDR) difference in AE level in the expected direction (AE het > AE homo, true positive), blue points indicate a significant difference in the opposite direction (AE het < AE homo, false positive), and the number of true and false positives is listed. c Boxplot of the percentage of individuals showing allelic imbalance (AE > 0.25) who are either heterozygous or homozygous for the top eQTL at each eGene before and after QC measures. Outliers are hidden for ease of viewing. d Mean percentage of het-SNPs that are found within heterozygous eGenes in bins of AE across individuals before and after QC measures. Error bars represent the standard error of the mean, and asterisks indicate a significant difference (1 % FDR) after applying QC measures for that bin

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