Skip to main content

Table 3 The number of genes with expression levels in blood of young healthy pigs that were significantly (q < 0.20) associated with observed phenotypes, with or without accounting for blood cell composition, the estimated number of genes that did not follow the null-hypothesis, and the relationship of adjusted estimates from two expression residuals across all genes

From: Quantitative analysis of the blood transcriptome of young healthy pigs and its relationship with subsequent disease resilience

Trait measured during each phase a Number of genes from expression residuals with or without adjustment for cell composition Correlation of estimates
Without With With+Without b
Quarantine Nursery
 qNurHS1 395 (1656) c 29 (1106) 395 0.92
 qNurHS2 171 (982) 101 (0) 173 0.93
 Growth rate 744 (3224) 830 (3357) 856 1.00
Challenge Nursery
 Health score 0 (0) 0 (0) 0 0.94
 Treatment rate 0 (0) 0 (0) 0 0.96
 Mortality + treatments 347 (3138) 170 (2956) 349 0.99
 Mortality 7 (2592) 2 (2649) 7 1.00
 Growth rate 0 (0) 0 (0) 0 0.98
Challenge Finisher
 Health score 0 (1048) 6 (1632) 6 1.00
 Treatment rate 0 (176) 0 (48) 0 0.99
 Mortality + treatments 0 (2014) 0 (1907) 0 0.99
 Mortality 0 (2900) 0 (2787) 0 0.99
 Growth rate 0 (0) 0 (0) 0 0.97
 Feed intake 0 (270) 0 (0) 0 0.98
 Feed intake duration 0 (0) 0 (0) 0 0.97
 Feed conversion rate 422 (2768) 1 (1373) 422 0.95
 Residual feed intake 0 (1892) 0 (1569) 0 0.97
Overall Challenge
 Treatment rate 0 (0) 0 (0) 0 0.98
 Mortality + treatments 40 (2663) 0 (2152) 40 0.99
 Mortality 1725 (5152) 1458 (5298) 1794 0.99
Carcass
 Carcass weight 0 (353) 0 (0) 0 0.96
 Dressing proportion 0 (0) 0 (0) 0 0.96
 Lean yield 42 (3912) 3 (2593) 42 0.97
 Carcass backfat 18 (3555) 1 (2827) 18 0.97
 Carcass loin depth. 0 (290) 0 (395) 0 0.99
  1. Abbreviations: qNurHS1 and qNurHS2, health scores in the quarantine nursery
  2. a Health score was recorded by 1 (pigs in perfect health) and 0 (pigs with clinical signs); Mortality with treatments was recorded by 0 (pigs that survived without any treatment) and 1 (pigs that died during a given period); Mortality was recorded by 0 (survival) and 1 (death)
  3. b The number of genes that were significant for at least one of the models with or without accounting for blood cell composition
  4. c The number of significant genes (q < 0.20) from expression residuals with or without adjustment for cell composition and, within parentheses, the estimated number of genes that did not follow the null-hypothesis using the method descibed in [21]