In agreement with prior observations of smaller lincRNA annotation sets, our analyses of the expanded lincRNA catalog presented here revealed that most lincRNAs are expressed at lower levels than protein coding genes [16], [19]. Though most lincRNAs are expressed at only a few copies per cell, we found that many lincRNAs are highly expressed with nearly 4,000 expressed at >FPKM 10 and nearly 1,000 expressed at >FPKM 30, rivaling the expression of many messenger RNAs. We chose to apply an expression cutoff to remove very lowly expressed transcripts from the catalog of lincRNAs. However, it may be the case that there exist many functional lincRNAs with very low expression levels, below our expression filter cutoff. For example, the functional human lincRNA HOTTIP is expressed in approximately one out of three cells [37]. Furthermore, recent findings have shown that the intergenic transcriptome may be vastly more complex than currently appreciated when very lowly expressed transcripts are considered [7]. It is possible that some of these are functional transcripts despite their apparent low expression, perhaps having brief bursts of expression during stages
