Table S4. Novel and known gene splice forms in the sixteen tissues, determined by comparison to the ENSEMBL v.61 annotation database using the program Cuffcompare.
Cuffcompare compares each predicted transcript’s intron chain against those of the reference transcripts and classifies the transfrag as: ‘equal’ to a reference transcript, if their intron chains are identical; ‘contained’, if included in a reference transcript’s; or as a ‘new splice form’, if the intron chain has at least one splice junction in common with the reference transcripts (n.b., other Cuffcompare codes are not relevant and were omitted).
| Set | Comparison to ENSEMBL v.61 | ||
|---|---|---|---|
| Full-length (Equal) | Partial (Contained) | New splice forms | |
| Adrenal | 5,705 | 22,613 | 22,592 |
| Adipose | 5,593 | 22,293 | 11,233 |
| Brain | 6,497 | 20,673 | 19,329 |
| Breast | 5,665 | 24,190 | 13,665 |
| Colon | 4,689 | 28,715 | 9,310 |
| Heart | 6,103 | 17,614 | 11,701 |
| Kidney | 5,501 | 26,615 | 11,775 |
| Liver | 4,483 | 24,563 | 7,692 |
| Lung | 4,958 | 33,735 | 12,346 |
| Lymph | 4,574 | 33,682 | 14,364 |
| Ovary | 7,017 | 18,667 | 18,048 |
| Prostate | 5,673 | 27,183 | 12,470 |
| Skel_muscle | 3,318 | 33,999 | 4,999 |
| Testes | 7,077 | 23,648 | 17,306 |
| Thyroid | 6,487 | 21,098 | 16,667 |
| White_blood | 4,568 | 25,004 | 6,533 |