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Figure 3

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mRNA decay is influenced by different elements in different cell types.

(A) Scatter plots comparing mRNA half lives in C2C12 with those in pluripotent and differentiating embryonic stem (ES) cells [10]. ES/LIF− and ES/RA+ represent ES cells differentiated by withdrawal of Leukemia Inhibitory Factor (LIF) and addition of Retinoic Acid (RA), respectively. Pearson correlation coefficient (r) and P-value for linear regression are shown for each plot. (B) Heat maps showing significance of hexamers associated with mRNAs with short (left panel) and long (right panel) half lives in C2C12, ES, ES/LIF−, and ES/RA+. Top 20 ranked hexamers for each cell type were selected and combined to illustrate variable significance in different cells. Each hexamer has a Significance Score (SS). SS = −log(P-value)*s, where P-value was derived from Fisher's exact test, and s = 1 if the hexamer is significantly associated with mRNAs with short half life, and  = −1 otherwise. SS are shown in the heat map with color according to the scale shown in the figure. Hexamers were clustered (Euclidean distance and average linkage) for easy visualization.

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