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Table 1 Heritability estimate and diet intraclass correlation summary statistics for all expressed genes and DEGs

From: Altered macronutrient composition and genetics influence the complex transcriptional network associated with adiposity in the Collaborative Cross

Heritability estimate or diet ICC Mean ± SE Median (Q1, Q3) Min Max
rI full — all expressed genes 0.327 ± 0.002 0.295 (0.157, 0.471) −0.12 0.991
rI full — diet DEGs 0.341 ± 0.005 0.327 (0.202, 0.471) −0.091 0.848
rI full — strain DEGs 0.387 ± 0.002 0.348 (0.232, 0.513) 0.087 0.991
rI HP— all expressed genes 0.324 ± 0.002 0.305 (0.136, 0.498) −0.332 0.99
rI HP — diet DEGs 0.339 ± 0.006 0.34 (0.179, 0.497) −0.288 0.899
rI HP — strain DEGs 0.388 ± 0.002 0.367 (0.221, 0.545) −0.194 0.99
rI HS — all expressed genes 0.328 ± 0.002 0.313 (0.146, 0.498) −0.359 0.993
rI HS —diet DEGs 0.348 ± 0.006 0.345 (0.203, 0.5) −0.264 0.887
rI HS — strain DEGs 0.389 ± 0.002 0.372 (0.228, 0.539) −0.234 0.993
g2 full — all expressed genes 0.218 ± 0.002 0.173 (0.085, 0.308) −0.056 0.983
g2 full — diet DEGs 0.221 ± 0.004 0.195 (0.112, 0.308) −0.044 0.735
g2 full — strain DEGs 0.26 ± 0.002 0.211 (0.131, 0.345) 0.045 0.983
g2 HP — all expressed genes 0.223 ± 0.002 0.18 (0.073, 0.331) −0.142 0.98
g2 HP — diet DEGs 0.226 ± 0.005 0.205 (0.098, 0.331) −0.126 0.816
g2 HP — strain DEGs 0.267 ± 0.002 0.224 (0.124, 0.374) −0.089 0.98
g2 HS — all expressed genes 0.224 ± 0.002 0.186 (0.079, 0.331) −0.152 0.985
g2 HS — diet DEGs 0.232 ± 0.005 0.208 (0.113, 0.333) −0.116 0.797
g2 HS — strain DEGs 0.267 ± 0.002 0.229 (0.129, 0.369) −0.105 0.985
Diet ICC — all expressed genes 0.055 ± 0.001 0.015 (−0.009, 0.079) −0.017 0.799
Diet ICC — diet DEGs 0.266 ± 0.003 0.235 (0.172, 0.327) 0.099 0.799
Diet ICC — strain DEGs 0.061 ± 0.001 0.019 (−0.008, 0.089) −0.017 0.787
  1. Post-diet heritability estimates were calculated from linear models including strain, diet, and week as covariates (rI or g2 “full”) for gene expression of the 11,542 expressed genes used in limma differential gene expression analysis. Diet-specific estimations of broad sense heritability were also calculated accordingly for gene expression levels represented by intraclass correlations (rI) and coefficients of genetic determination (g2) for each trait using the MSB and MSW for strain derived from linear models with strain and week as covariates using only data from each experimental diet per model as indicated to assess how different diet “environments” affect heritability. The intraclass correlation for diet (Diet ICC), which is the proportion of the total phenotypic variation that is accounted for by differences between diet, was calculated to compare the proportion of variation in gene expression attributed to diet in general or genetics. Summary statistics were calculated for each group of genes after heritability estimates, and diet ICC were obtained. g2 accounts for the additive genetic variance that doubles during inbreeding and may be a more appropriate estimate for broad sense heritability in this study. However, both rI and g2 values are presented to facilitate comparisons with other findings in the literature