of FPKM>10 lincRNAs, and 67.7% of FPKM>30 lincRNAs are greater than 30 kilobases from the nearest protein coding gene on either strand. We annotated the lincRNAs as belonging to the same “group” (see Methods) if they are within 1 kilobase of each other to account for the possibility that some proximal lincRNA annotations may be partial structures of larger transcripts (see Discussion). This grouping resulted in 35,585 distinct lincRNA groups at FPKM>1, 2,970 at FPKM>10, and 764 at FPKM>30, and the lincRNAs in the catalog are named according to these groups (Dataset S2). These annotations are likely to be incomplete due to limitations in transcript assembly from RNA-seq data; indeed, some annotations may be fragments of larger overlapping lincRNA transcripts. Therefore, the actual number of independent lincRNAs may differ from the above numbers, and future work is needed to more fully define complete, independent lincRNA transcript annotations (see Discussion).
