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Fig. 3 | BMC Genomics

Fig. 3

From: Identification and analysis of ribosome-associated lncRNAs using ribosome profiling data

Fig. 3

The discrimination of ribosome-associated and ribosome-free lncRNAs by ribosome density in the HeLa dataset. a Kernel density distribution of ribosome density (log2 scale) for 3 UTRs (gray), CDSs (blue), and lncRNAs (red). The vertical dashed line corresponds to the 90th percentile of the ribosome density scores for 3 UTRs, which is used as the cut-off to distinguish between ribosome-associated lncRNAs and ribosome-free lncRNAs. Those lncRNAs to the right of this cut-off (including the cut-off itself) are identified as ribosome-associated lncRNAs; the rest are ribosome-free in this study. Note that transcripts or regions without any mapped Ribo-seq read correspond to a peak near -33 (owing to the addition of a pseudo value of 10e-10 prior to log transformation). b Violin plot of the expression levels (RPKM, log2 scale) of mRNAs as well as ribo-associated and free lncRNAs. The p-values correspond to two-sample t-tests. c Classification of lncRNAs by using FLOSS, RRS, and Framescore as filters to assess the coding potential for each ribosome-associated lncRNA. “F” means ribosome-free, “A0” means no coding filter has been passed, “A1”, “A2”, and “A3” denote that one, two, and three passed translation filter(s), respectively. (See Additional file 9 for the other datasets)

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