Figure 3

Gene expression reproducibility is dependent on expression level. A) Example genes showing good (CBNL2, left) and poor (TCF15, right) reproducibility using microarray. Reproducibility is defined here based on the between-brain correlation of a gene on average log2(intensity) values in each of the 29 brain regions. B) There is a strong relationship between expression level and reproducibility for genes with low expression. Genes were sorted from lowest to highest expression and divided into 20 bins based on expression, which each represent 5% of array genes (x-axis). Each point shows the average between-brain correlation (as in A) for all genes in that bin (y-axis), as measured by microarray (blue) and RNA-Seq (green). Arrows indicate approximate average TPM and intensity values below which RNA-Seq (TPM = 1) and microarray (log2(intensity) = 5) become progressively less reliable. Approximately 25% and 33% of genes have expression levels below these thresholds in RNA-Seq and microarray, respectively. The standard error of the mean (SEM) for each bin is smaller than the dot size.