Table 1.
Alternative splicing events detected in protein coding genes and pseudogenes implicated in cancer.
| Alternative splicing event | Protein coding genes | CanGEM gene list (31057 entries) | % cancer protein coding genes |
|---|---|---|---|
| Cassette exon (CE) | 13506 | 11771 | 87 |
| Intron retention (IR) | 8190 | 6775 | 83 |
| Alternative 3′ss (A3SS) | 6701 | 5685 | 85 |
| Alternative 5′ss (A5SS) | 6624 | 5640 | 85 |
| Alternative first exons (AFE) | 8050 | 7136 | 89 |
| Alternative last exons (ALE) | 3631 | 3233 | 89 |
| Mutually exclusive exons (MXE) | 3376 | 3006 | 89 |
|
| |||
| Alternative splicing event | Pseudogenes | CanGEM gene LIST (31057 entries) | % cancer pseudogenes |
|
| |||
| Cassette exon (CE) | 434 | 139 | 32 |
| Intron retention (IR) | 465 | 187 | 40 |
| Alternative 3′ss (A3SS) | 241 | 91 | 38 |
| Alternative 5′ss (A5SS) | 218 | 82 | 38 |
| Alternative first exons (AFE) | 91 | 27 | 30 |
| Alternative last exons (ALE) | 104 | 32 | 31 |
| Mutually exclusive exons (MXE) | 50 | 16 | 32 |
Homo sapiens genes (GRCh37.p10) dataset (62252 total genes) was used to filter alternative splicing events in protein coding genes (22719 entries) and pseudogenes (14775 entries) and verified their presence in the Cancer GEnome Mine database (31057 entries—CanGEM, http://www.cangem.org/).