Figure 4
Identification and characterization of lncRNAs in lymphoid eRNA regions (A) Quantification of expressed protein-coding genes, lncRNA genes, annotated lncRNA genes (in GENCODE V19 or LNCipedia database), and novel lncRNA genes (not annotated in these databases). (B) Size distribution of novel lncRNA transcripts. Data for transcripts from protein-coding databases and annotated lncRNA databases are depicted for comparison. (C) Expression of protein-coding genes, annotated and novel lncRNA genes (previously defined), and hybrid lncRNA genes (the subset of annotated lncRNA genes for which we discovered previously unknown transcripts) presented as the maximum FPKM values (of 20 samples). Red crosses indicate the mean, green squares indicate the median, and the outline indicates range. (D) Violin plot of transcript expression levels. For each transcript, the maximum expression value was used for the plot. Type 1, novel transcripts from novel loci or annotated loci; Type 2, transcripts from annotated loci that have novel isoforms; Type 3, annotated transcripts from known loci. Expression levels were higher for novel lncRNA transcripts than for annotated lncRNA transcripts. (E) Expression of newly identified lncRNA genes in BM and thymus samples (left) and 10 samples from the Human BodyMap project (right; Table S5).
