A complete statistical model for calibration of RNA-seq counts using external spike-ins and maximum likelihood theory
Fig 7
Differential gene expression in Ciona embryonic differentiation study.
(A) Diagnostic histogram of p-values for null hypothesis of no differential gene expression between the FgfrDN and LacZ cell types. (B) Fold change (log2 scale) for the FgfrDN/lacZ comparison. The vast majority of the significant (FDR = 0.01) transcripts were down-regulated in the FgfrDN cell type, 4,778 out of 4,493. The average fold change for up- and down-regulated transcripts was 2.5 and 1.9, respectively. (C) Similar to panel A, but for the null hypothesis of no differential gene expression between the FgfrDN and M-RasCA cell types. (D) Fold change, similar to panel B, but for the M-RasCA/FgfrDN comparison. 1,934 transcripts differentially expressed at an FDR value of 0.01 (corresponding cutoff p-value equal to 0.0017). Of the 1,934 significant (FDR = 0.01) fold changes, 1,560 were greater than 1, and 374, less than 1. The average fold change for up- and down-regulated transcripts was 1.9 and 2.8, respectively.