Fig. 1

This figure provides an initial visual analysis of gene expression patterns found in liver of 12 embryos (E16, E18 and E20) and 12 hatchlings (D1, D3 and D9) during the critical embryo-to-hatchling transition. GeneSpring GX 7 software was only used for the preliminary analysis of differentially-expressed (FDR ≤ 0.01) genes (DEGs) and visualization of expression patterns from hierarchical (a) and k-means cluster (b) analyses. The heat map in Panel a clearly shows three distinct expression patterns of DEGs: Cluster A (high in embryos, low in hatchlings), Cluster B (low in embryos, high in hatchlings) and Cluster C (mixed pattern). K-means clustering (Panel b) provides higher resolution of DEGs found in Cluster A, including two examples: deiodinase 3 (DIO3) and monoacylclycerol O-acyltransferase 1 (MOGAT1), both have higher expression in embryos and lower abundance in hatchlings. In contrast, Cluster B contains DEGs with lower expression in embryos [i.e., deiodinase 2 (DIO2)] and much greater (log-scale) abundance in liver of hatchlings [i.e., thyroid hormone-responsive Spot 14 protein alpha (THRSPA)], especially in fully-fed D3 and D9 chicks