Table 2. Distribution of DEGs among core Orthologs, Other Orthologs, and Lineage-Specific Genes.
| Species | % of DEGs in core Genes | % of DEGs in Other Ortho Genes | % of DEGs in Lineage-Specific Genes | DEG Enrichment Fold in core Genes | Chi-Squared P Value | DEG Enrichment Fold in Other Ortho Genes | Chi-Squared P Value | DEG Enrichment Fold in Lineage-Specific Genes | Chi-Squared P Value |
|---|---|---|---|---|---|---|---|---|---|
| P. vulgaris | 52.77 | 26.23 | 21.00 | 1.13 | 8.40e–33 | 1.02 | 2.32e+00 | 0.76 | 1.20e–46 |
| R. communis | 47.99 | 30.99 | 21.03 | 1.04 | 1.74e–04 | 1.03 | 3.38e–01 | 0.89 | 9.79e–12 |
| Arabidopsis | 51.05 | 23.12 | 25.83 | 1.10 | 2.06e–40 | 1.01 | 3.14e+00 | 0.84 | 1.78e–51 |
| H. annuus | 38.86 | 22.02 | 39.12 | 1.18 | 7.60e–47 | 1.16 | 3.97e–17 | 0.81 | 5.95e–92 |
| S. lycopersicum | 42.68 | 23.67 | 33.65 | 1.13 | 6.07e–27 | 1.13 | 6.91e–12 | 0.81 | 1.64e–61 |
| B. vulgaris | 46.83 | 22.07 | 31.10 | 1.20 | 3.11e–46 | 1.13 | 9.81e–09 | 0.75 | 5.46e–81 |
| All | 1.16 | 9.53e–257 | 1.10 | 1.20e–43 | 0.77 | 0.00e+00 |
Significance of enrichment (fold >1) or depletion (fold <1) was assessed using a chi-squared test followed by a Bonferroni correction for multiple testing.