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

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

Trait measured during each phase ^a	Number of genes from expression residuals with or without adjustment for cell composition			Correlation of estimates
Trait measured during each phase ^a	Without	With	With+Without ^b	Correlation of estimates
*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

Abbreviations: qNurHS1 and qNurHS2, health scores in the quarantine nursery
^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)
^b The number of genes that were significant for at least one of the models with or without accounting for blood cell composition
^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]

ISSN: 1471-2164