Table 1.
Number of differentially expressed gene between AI and NT samples by analysis and sign of the pattern.
| Individual analyses | Meta-analyses | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| d280X1 | d7E | d25X | d25E | Study | Sample | ||||||||
| + | − | + | − | + | − | + | − | + | − | + | − | ||
| d280X | + | 1892 | − | 03 | 1 | 1 | 0 | 1 | 1 | 2 | 0 | 3 | 0 |
| − | − | 657 | 1 | 2 | 0 | 1 | 0 | 0 | 0 | 14 | 1 | 19 | |
| d7E | + | 0.0%4 | 1.9% | 52 | − | 0 | 0 | 0 | 4 | 0 | 0 | 26 | 0 |
| − | 1.4% | 2.7% | − | 74 | 0 | 0 | 0 | 1 | 0 | 0 | 1 | 26 | |
| d25X | + | 4.5% | 0.0% | 0.0% | 0.0% | 22 | − | 0 | 1 | 0 | 0 | 0 | 0 |
| − | 0.0% | 7.1% | 0.0% | 0.0% | − | 14 | 0 | 0 | 0 | 0 | 0 | 1 | |
| d25E | + | 10.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 10 | − | 0 | 0 | 0 | 0 |
| − | 2.6% | 0.0% | 10.5% | 2.6% | 2.6% | 0.0% | − | 38 | 0 | 1 | 4 | 1 | |
| Study | + | 3.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 66 | − | 9 | 0 |
| − | 0.0% | 13.7% | 0.0% | 0.0% | 0.0% | 0.0% | 0.0% | 1.0% | − | 102 | 0 | 10 | |
| Sample | + | 1.5% | 0.5% | 12.7% | 0.5% | 0.0% | 0.0% | 0.0% | 2.0% | 4.4% | 0.0% | 204 | − |
| − | 0.0% | 10.8% | 0.0% | 14.8% | 0.0% | 0.6% | 0.0% | 0.6% | 0.0% | 5.7% | − | 176 | |
d280X = day 280 extra-embryonic samples, d7E = day 7 embryos, d25X = day 25 extra-embryonic sample, d25E = day 25 embryos.
Number of differentially expressed genes between AI and NT (P-value < 1×10−3, fold change > 1.23) within individual-experiment analyses, study-level standardized (Study), and sample-level (Sample) meta-analysis (diagonals). “+” denotes over-expression in AI relative to NT and “−” denotes under-expression in AI relative to NT.
Upper off-diagonals are the number of genes identified differentially expressed in all pairs of analyses relative to the maximum number of significant genes that can overlap in both analyses.
Lower off-diagonals are the percentage of genes identified differentially expressed in all pairs of analyses relative to the maximum number of significant genes that can overlap in both analyses.