Supplementary Figure 3: Changes in gene expression between balancer and wild-type haplotypes.
From: Highly rearranged chromosomes reveal uncoupling between genome topology and gene expression
a, Change in gene expression (balancer/wild-type, log2 fold change) in F1 heterozygous and single balancer (CyO only or TM3 only) adult fly heads (mixed sexes). Genes with significant (two-sided Wald test, 5% FDR) effect of genotype on differential expression (DE-genes) highlighted in blue, Pearson correlation coefficient (r) indicated. b, Same as (a), but comparing F1 heterozygous adult female heads to mixed sex heads as a proxy for expected biological noise. c, Change in allele-specific gene expression (log2 fold change) for testable genes with exons overlapping an allele-specific deletion or duplication. Fully duplicated genes are shown separately in Fig. 2b. Points, individual genes (180 genes partially deleted in balancer, 116 partially deleted in wild-type, 13 partially duplicated in balancer, 14 partially duplicated in wild-type); center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; dashed lines, two-fold increase or decrease.
