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. Author manuscript; available in PMC: 2016 Aug 6.
Published in final edited form as: Mol Cell. 2015 Aug 6;59(3):413–425. doi: 10.1016/j.molcel.2015.06.036

Figure 2. Transcriptome-wide loss in mRNA selectivity for Upf1 ATPase cycle mutants.

Figure 2

(A-C) Scatter plots of reads per kilobase transcript per million mapped reads (RPKM) from RNA-seq of input samples versus IPs for Flag-Upf1 WT (A), DEAA (B) and KA (C). Genes with IP/input ratios for WT Upf1 of greater than 2.05 (cut-off based on 5% false discovery rate (FDR) established using cells expressing Flag epitope only, Figure S2) are shown in red (Upf1-enriched), while genes with log2 (IP/input) between −0.5 and +0.5 are shown in blue (non-enriched). All remaining genes are shown in grey.

(D) Cumulative fraction of Upf1-enriched and non-enriched genes with IP enrichment represented as log2 (IP RPKM/input lysate RPKM) for Flag-Upf1 WT, KA, and DEAA, along with Flag only. Difference between WT Upf1 (Upf1-enriched) curve compared to all other curves was statistically significant (p-value <0.05 for all comparisons, KS-test).

See also Figure S2 and Table S1