Fig. 3

Differentially expressed genes show length-dependent misregulation in topotecan datasets but not in MeCP2 studies. a Scatter plot of log fold change in expression between topotecan and vehicle-treated cultured cortical neurons (y-axis) against its gene length (x-axis) in RNA-seq data from King et al.¹⁰ (left panel; n = 5 each; FDR < 0.05) and Mabb et al.¹⁹ (right panel; n = 3 each; FDR < 0.01). b Scatter plot of log fold change in expression (microarray) between C57BL KO and its C57BL WT littermates (y-axis) against its gene length (x-axis) in hypothalamus²² (left panel; n = 4 each; FDR < 0.05 and log₂FC > 0.2) and cerebellum²¹ (right panel; n = 4 each; FDR < 0.05 and log₂FC > 0.2). c Scatter plot of log fold change in expression (microarray) between FVB Tg to its FVB WT littermates (y-axis) against gene length (x-axis) in hypothalamus²² (n = 4 each; FDR < 0.05 and log₂FC > 0.2) and cerebellum²¹ (n = 4 each; FDR < 0.05 and log₂FC > 0.2). d Scatter plot of log fold change in expression between KO or Tg and WT littermates (y-axis) against gene length (x-axis) in RNA-seq datasets: Hypothalamus KO/WT comparison²³ (left panel; n = 3 each; FDR < 1e−5) and hypothalamus Tg/WT comparison²³ (right panel; n = 3 each; FDR < 1e−5). Red dots indicate long genes and blue dots indicate short genes. Differentially expressed genes were obtained from the published gene lists. See Supplementary Fig. 5 for additional analyses from published MeCP2 datasets