Fig. 4.

TOC refines classification of lncRNAs. (A) TOC-based classification improves previous lncRNA predictions. Shown are RNA-seq and ribosome profiling read densities associated with three putative lncRNAs (Ulitsky et al., 2011), which had conflicting annotations in published zebrafish lncRNA sets (Pauli et al., 2012; Ulitsky et al., 2011). Transcript structures are shown in black. Introns are indicated as dashed lines. The region scoring highest in PhyloCSF (Lin et al., 2011) is indicated in orange. Whereas TOC reveals the protein-coding nature of linc-ca2, it confirms the non-coding nature of the two conserved lncRNAs megamind and cyrano. These two lncRNAs had been filtered out in the Pauli et al. lncRNA set owing to their relatively high phylogenetic codon substitution frequency scores (PhyloCSF >20). (B) Fraction of loci that are classified by TOC as coding (blue), leader-like (green) and trailer-like (red) in three collections of lncRNAs: ZF1 (Pauli et al., 2012), ZF2 (Ulitsky et al., 2011) and mESCs (Guttman et al., 2011).