Table 3. Ten Paired Comparisons between RNA-Seq Samples and Identified Number of DEGsa.
| paired comparison | DEGs (χ2-test) | DEGs (edgeR) | DEGs overlapped |
|---|---|---|---|
| C1 (S1 vs S2) | 63 | 13 | 13 |
| C2 (S1/2 vs S3) | 50 | 25 | 25 |
| C3 (S3 vs S4) | 111 | 47 | 46 |
| C4 (S1/S2 vs S4) | 67 | 41 | 41 |
| C8 (S5 vs S6) | 14 | 8 | 8 |
| C9 (S6 vs S7) | 201 | 64 | 62 |
| C10 (S5 vs S7) | 137 | 42 | 42 |
| C5 (S1/2 vs S5) | 356 | 168 | 129 |
| C6 (S3 vs S6) | 481 | 387 | 273 |
| C7 (S4 vs S7) | 1265 | 941 | 627 |
a
This table shows the number of DEGs in each paired comparison highlighting the conditions (C5, C6, C7) attributing to the effect of changes in circuit plasmid copy number. S1/2 represents means of the gene expression values of the two replicate Samples 1 and 2. Ten paired comparisons performed among the 7 samples: C1 is for studying RNA-Seq repeatability between biological replicates (S1 vs S2); C2, C3, C4 are grouped for studying different circuit loads in the medium copy plasmid (pSB3K3); and C8, C9, C10 are grouped for studying different circuit loads in the low copy plasmid (pSB4K5); C5, C6, and C7 are grouped for studying the effect caused by changes in plasmid copy number of the same circuit.