Figure 2.

Comparison of RNA-Seq and microarray analyses showed that RNA-Seq identified more differentially expressed genes across cell types than microarray. A, Spearman's rank correlation between gene expression data obtained by the RNA-Seq and microarray methods across cell types. Gene expression profiles of the same cell type obtained by the RNA-Seq and microarray methods showed a high degree of correlation. B, Numbers of differentially expressed genes identified by the RNA-Seq and microarray methods. A snapshot of the data is summarized in the Venn diagram. Using a fourfold difference as the cutoff, RNA-Seq analysis identified 3129 genes as differentially expressed by astrocytes, whereas microarray identified only 1367 genes. The majority of genes identified by microarray as differentially expressed are similarly classified by RNA-Seq (1279). RNA-Seq identified an additional 1850 genes as differentially expressed that were not identified by microarray as differentially expressed. C–E, RNA-Seq versus microarray comparisons for neurons, oligodendrocytes, and microglia. F, The relationship between fold enrichment and expression level in astrocytes. There is a sharp cutoff line on the left (FPKM = 0.1 or −3.3 on the log2 scale) because we set any FPKM value <0.1 to 0.1 to avoid ratio inflation in fold enrichment calculations. G, The relationship between fold enrichment and expression level in astrocytes.