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Table 1 Differential transcript analysis Hi-Seq

From: Comparison of triple-negative breast cancer molecular subtyping using RNA from matched fresh-frozen versus formalin-fixed paraffin-embedded tissue

Transcript Type All Transcripts Differential Transcripts (%) FFPE (%) FF (%)
rRNA 44 42 (95.5%) 40 (95.2%) 2 (4.8%)
Misc RNA 437 412 (94.3%) 412 (100.0%) 0 (0.0%)
snoRNA 326 307 (94.2%) 306 (99.7%) 1 (0.3%)
snRNA 410 383 (93.4%) 383 (100.0%) 0 (0.0%)
Sense intronic 513 449 (87.5%) 448 (99.8%) 1 (0.2%)
3′ overlapping ncrna 8 7 (87.5%) 7 (100.0%) 0 (0.0%)
miRNA 232 194 (83.6%) 192 (99.0%) 2 (1.0%)
mt RNA 10 7 (70.0%) 4 (57.1%) 3 (42.9%)
Pseudogene 3661 2504 (68.4%) 2348 (93.8%) 156 (6.2%)
Antisense 2881 1949 (67.7%) 1906 (97.8%) 43 (2.2%)
Sense overlapping 116 63 (54.3%) 63 (100.0%) 0 (0.0%)
lincRNA 1992 1041 (52.3%) 1009 (96.9%) 32 (3.1%)
Processed transcript 300 138 (46.0%) 129 (93.5%) 9 (6.5%)
Polymorphic pseudogene 17 7 (41.2%) 3 (42.9%) 4 (57.1%)
Protein coding 16,630 4450 (26.8%) 2112 (47.5%) 2338 (52.5%)
Total 27,577 11,953 (43.3%) 9362 (78.3%) 2591 (21.7%)