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. Author manuscript; available in PMC: 2021 May 23.
Published in final edited form as: Nat Struct Mol Biol. 2020 Nov 23;28(1):62–70. doi: 10.1038/s41594-020-00526-w

Figure 2. The TET2-bound transcriptome.

Figure 2.

(A) Clustered heatmap showing the Pearson’s correlation coefficients between reads per kilobase per million (RPKMs) calculated on all annotated genes in input and TET2 CLIP from all replicates.

(B) Enrichment of transcripts in TET2 CLIP-seq. Black semi-transparent circles represent all detected RNAs. Transcripts annotated as tRNAs are highlighted in red. Mean RPKMs from input sample and CLIP are plotted on the x and y axis, respectively.

(C) Odds ratio for classes of > 2-fold enriched RNAs in TET2 CLIP. Fisher’s one-sided test P-values are indicated, when significant (P < 0.05). Only transcripts detected (> 1 read) in at least one replicate were considered. snRNA, small nuclear RNAs; rRNA, ribosomal RNAs; miRNA, micro RNAs; lncRNA, long noncoding RNAs; misc, RNAs not included in the other displayed categories; pseudo, pseudogene-derived RNAs; snoRNA, small nucleolar RNAs; scaRNA, small Cajal body RNAs; mRNA, protein-coding messenger RNAs.

(D) Same as (C) but considering only RNAs containing a peak (see text for details) with FDR-corrected P-value < 10−5 as enriched.

Data are from four replicates: two independent immunoprecipitations from each of two independently generated epitope-tagged clones (clone 65 and 75).