In order to minimize any potential contamination of the lincRNA catalog with protein coding transcripts, the filtering approach used was very aggressive. In fact, most previously annotated noncoding RNAs failed to pass our filters and were therefore excluded from the lincRNA catalog (Table S3 and Dataset S9). The vast majority of these transcripts (including most GENCODEv6 “lincRNAs” and “processed transcripts”) overlap known or predicted protein coding genes, pseudogenes, or non-lincRNA noncoding RNAs (e.g. microRNAs)(Table S3). Some of these removed transcripts may be functional long noncoding RNAs, such as GAS5 (removed because it contains 10 snoRNA genes within its introns). However, in order to most confidently identify only lincRNAs, rather than potential unannotated extensions of known genes, these were removed.
