Table 1 Cancer RNA-seq datasets used for benchmarking
From: ChimPipe: accurate detection of fusion genes and transcription-induced chimeras from RNA-seq data
Cancer dataset | Cell line | Tumor type | Number of validated | Number of validated | Number of different | SRAa accession |
|---|---|---|---|---|---|---|
fusion genes | fusion junctions | libraries | codes | |||
Berger | K-562 | Leukemia | 3 | 3 | 2 | SRR018268, |
SRR0182689 | ||||||
501 Mel | Melanoma | 4 | 5 | 1 | SRR018266 | |
M000216 | 1 | 1 | 1 | SRR018259 | ||
M000921 | 2 | 3 | 1 | SRR018267 | ||
M010403 | 1 | 1 | 1 | SRR018265 | ||
M980409 | 1 | 1 | 1 | SRR018261 | ||
M990802 | 2 | 2 | 1 | SRR018260 | ||
All | All | 14 | 16 | - | - | |
Edgren | KPL-4 | Breast cancer | 3 | 3 | 1 | SRR064287 |
MCF-7 | 6 | 8 | 1 | SRR064286 | ||
BT-474 | 21 | 25 | 2 | SRR064438, | ||
SRR064439 | ||||||
SK-BR-3 | 10 | 10 | 2 | SRR064440, | ||
SRR064441 | ||||||
All | 40 | 46 | 1 | - |