Table 2.
| LncRNAs upregulated in all three genetic lines (>2 fold) upon infection and their expression correlation with protein coding genes | |||||||
|---|---|---|---|---|---|---|---|
| LncRNA feature ID | Resistant line |
Control line |
Susceptible line |
Correlation with (R2) | |||
| EDGE test: Fold change | FDR p-value correction | EDGE test: Fold change | FDR p-value correction | EDGE test: Fold change | FDR p-value correction | ||
| Omy200117486 | 24.36 | 0 | 41.6 | 0 | 91.18 | 0 | Interferon-induced guanylate-binding protein 1 (0.82) |
| Omy100128008 | 14.95 | 0 | 22.23 | 0 | 46.4 | 0 | Complement protein component C7-1 (c7-1) (0.82) |
| Omy200138656 | 24.3 | 0.000001 | 11.63 | 0.011489 | 28.75 | 0 | Complement C5 (0.66) |
| Omy100149048 | 7.93 | 0.000004 | 5.95 | 0.048727 | 14.15 | 0 | Unknown |
| Omy200107378 | 6.38 | 0.000062 | 11.22 | 0.004248 | 11.22 | 0 | Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (0.92) |
| Omy200165911 | 3.68 | 0.049287 | 4.5 | 0.040404 | 9.98 | 0 | Unknown |
| Omy100052789 | 5.51 | 0.000564 | 5.13 | 0.047151 | 8.65 | 0 | Unknown |
| Omy200107535 | 3.71 | 0.000147 | 6.16 | 0.012707 | 8.12 | 0 | Nuclear factor of kappa light polypeptide gene enhancer in B-cells 2 (0.92) |
| Omy300025398 | 4.37 | 0.006514 | 5.15 | 0.002475 | 4.86 | 0 | Unknown |
| Omy300085997 | 3.68 | 0.000345 | 3.16 | 0.043867 | 4.02 | 0.001759 | Unknown |
| Omy200206941 | 3.16 | 0.000344 | 2.33 | 0.015415 | 3.44 | 0.000002 | Lysozyme C II precursor (0.83) |
| Omy300043066 | 3 | 0.000121 | 3.74 | 0.006748 | 3.03 | 0.000014 | Properdin (0.82) and complement factor b-like (0.89) |
| LncRNAs showing drastic (>100) fold change upon infection in one particular genetic line and associated gene in genome | |||||||
| Feature ID | EDGE test: Fold change | FDR p-value correction | Comparison | Classification of LncRNA | Associated Gene(s) (R2) | ||
| Upregulated upon infection | |||||||
| Omy200018785 | 136.06 | 0.001233 | D1_S_FP vs D1_S_PBS | Intergenic | |||
| Omy200132807 | 121.83 | 0.000167 | D5_S_FP vs D5_S_PBS | Intergenic | |||
| Omy100037031 | 105.28 | 0.012820 | D5_C_FP vs D5_C_PBS | Intergenic | |||
| Downregulated upon infection | |||||||
| Omy200194608 | −168.77 | 0.000001 | D1_S_FP vs D1_S_PBS | Genic, antisense | GSONMG00062425001 si:ch73- protein (0.27) | ||
| Omy200226560 | −121.90 | 0.001972 | D1_R_Fp vs D1_R_PBS | Genic, antisense | GSONMG00065518001 (fatty-acyl reductase-1) (0.36) | ||
| Omy100064313 | −108.56 | 0.001716 | D1_R_Fp vs D1_R_PBS | Intergenic | |||
LncRNAs upregulated in all three genetic lines (>2 fold) on 5th day post Fp challenge and their expression correlation with protein coding genes (top). LncRNAs showing highest fold change (>100-fold) upon Fp infection in at least one genetic line relative to the two other genetic lines and their associated protein coding gene in genome (bottom). Fold change was considered significant if FDR-corrected p value was less than 0.05.