Figure 4.

Gene Expression Analysis in A-T iPSC

(A) Volcano plot comparing changes in transcript (as log₂ fold change of fragments per kilobase of transcript per million mapped reads) and significance (−log₁₀ of the FDR) for Q3SA versus Q3SC. Sample names are color-coded by genotype: red for ATM^−/− and blue for ATM^+/−. The significance threshold of 5% FDR is shown as a horizontal dashed line (n = 2 per group). Smaller gray dots indicate transcripts with no significant difference. Colors of dots indicate whether transcripts overlap Q1SA versus Q3SC or not: see key and the colors of overlapping regions in the Venn diagram (C) for color interpretation.

(B) Volcano plot comparing Q1SA with Q3SC, with dot coloring to show overlap with Q1SA versus Q3SC.

(C) Venn diagram indicating the numbers of significantly different transcripts in each contrast and the numbers of overlaps among the contrasts.

(D) Pathway analysis of transcripts that are decreased in abundance in Q3SA compared with Q3SC (top) or increased (bottom). The bar indicates the p value calculated by Fisher’s exact test, and the color intensity depicts the ratio of pathway genes included in this differentially expressed set.