Table 4.
– Classification of expression patterns for DEGs
| G1 = G2 = G3 | G1 > G2 = G3 | G1 > G2 > G3 | G1 > G3 > G2 | G2 > G1 = G3 | G2 > G1 > G3 | G2 > G3 > G1 | G3 > G1 = G2 | G3 > G1 > G2 | G3 > G2 > G1 | Total | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| all_genes | 13.5 | 2.2 | 15.1 | 8.7 | 2.3 | 15.9 | 9.4 | 2.9 | 15.1 | 14.8 | 20689 |
| common | 0.0 | 0.1 | 23.2 | 5.8 | 0.2 | 26.4 | 5.7 | 0.7 | 18.6 | 19.2 | 2376 |
| EEE-E | 0.0 | 0.6 | 20.7 | 7.4 | 0.7 | 21.9 | 8.1 | 1.6 | 19.9 | 19.2 | 7247 |
| DDD-D | 0.0 | 0.4 | 25.0 | 7.3 | 0.6 | 25.0 | 6.0 | 1.4 | 17.3 | 17.1 | 3850 |
| SSS-S | 0.0 | 0.2 | 19.3 | 7.1 | 0.3 | 21.7 | 9.4 | 0.9 | 19.9 | 21.2 | 7295 |
| E-E (edgeR) | 0.0 | 0.6 | 20.4 | 7.3 | 0.7 | 22.1 | 8.3 | 1.6 | 19.7 | 19.3 | 7247 |
| edgeR_robust | 0.0 | 0.3 | 20.6 | 8.4 | 0.5 | 22.0 | 8.8 | 1.2 | 19.1 | 18.9 | 8076 |
| D-D (DESeq) | 0.0 | 0.4 | 24.3 | 7.2 | 0.6 | 24.2 | 6.0 | 1.4 | 17.8 | 18.1 | 3832 |
| S-S (DESeq2) | 0.0 | 0.2 | 20.4 | 8.0 | 0.3 | 21.8 | 8.9 | 0.8 | 19.7 | 19.9 | 7585 |
| voom | 0.0 | 0.7 | 21.3 | 7.7 | 0.7 | 22.5 | 8.2 | 1.3 | 18.7 | 19.0 | 7016 |
| SAMseq | 0.0 | 0.2 | 20.9 | 9.7 | 0.3 | 21.8 | 9.2 | 0.8 | 18.9 | 18.3 | 9453 |
| PoissonSeq | 0.0 | 0.0 | 19.5 | 8.9 | 0.1 | 22.2 | 9.4 | 0.3 | 20.3 | 19.3 | 6613 |
| baySeq | 0.0 | 0.8 | 21.0 | 5.5 | 1.3 | 23.7 | 6.3 | 2.8 | 19.0 | 19.6 | 3975 |
| EBSeq | 0.0 | 0.0 | 21.0 | 7.0 | 0.1 | 23.7 | 7.1 | 0.3 | 20.8 | 19.9 | 5699 |
Percentages of genes assigned to each of the ten possible patterns defined as baySeq. Numbers in the “Total” column indicate the numbers of genes. For example, baySeq assigned 13.5 % of 20,689 genes as “G1 = G2 = G3.”