An additional set of annotated lincRNA transcripts from Cabili et al. [16] passed all our filters except were not expressed at FPKM>1 in any of the datasets analyzed here and were therefore removed from the lincRNA catalog in Dataset S2. However, some of these transcripts were reported as expressed at FPKM>1 in at least one of the datasets analyzed in Cabili et al. [16], all of which are distinct from the datasets analyzed here. These additional lincRNAs were merged with the lincRNAs in the catalog in Dataset S2 resulting in an additional 920 lincRNAs in 741 groups at FPKM>1, 88 lincRNAs in 82 groups at FPKM>10, and 17 lincRNAs in 17 groups at FPKM>30. This expanded lincRNA catalog is in BED format for genome build hg18 in Dataset S3 and was not used further for any analyses in this study.
