Skip to main content
Fig. 2 | BMC Genomics

Fig. 2

From: Transcriptome analyses of liver in newly-hatched chicks during the metabolic perturbation of fasting and re-feeding reveals THRSPA as the key lipogenic transcription factor

Fig. 2

Initial hierarchical clustering analysis of differentially-expressed genes (DEGs) (P ≤ 0.05) identified in liver of newly-hatchling chicks during the fasting-refeeding perturbation (Panel a). This heat map, representing two-way hierarchical clustering of 1170 DEGs (Y-axis) across 10 treatment groups (X-axis), shows two major clusters of DE genes that are either up-regulated (Cluster A) or down-regulated (Cluster B) by fasting (4, 24 and 48 h) after hatch. In contrast, Cluster A genes are down-regulated in the fully-fed (FED) and refed (REFED) groups on day 3(D3) and D4, whereas Cluster B genes are up-regulated after refeeding and in FED groups on D2, D3 and D4. Panel b. K-means cluster plots of DEGs (log2 FC) identified in four contrasts of fasting [C1 = D1FED vs. D1FAST24h; and C2 = D2FED vs. D2FAST48h) and refeeding (C3 = D2FAST48h vs. D3REFED4h; and C4 = D2FAST48 vs. D3REFED24h). K-means analysis revealed two distinct gene expression patterns, each composed of four clusters of DEGs identified by microarray and statistical analysis. Four distinct K-means clusters of lipogenic genes were down-regulated by fasting and sharply rebounded at 4 h or 24 h after refeeding. In contrast, four other clusters represent lipolytic genes whose expression was up-regulated by fasting and sharply down-regulated after refeeding. The original responses showed positive or negative log2 FC values which represent down-regulation or up-regulation by fasting, respectively. Further, positive or negative log2 FC means indicates either down-regulation or up-regulation caused by re-feeding for either 4 h or 24 h after a 48 h fast, respectively. However, the log2 FC values shown here were multiplied by − 1 to make the relative expression (log2 fold-change) either positive for up-regulation or negative for down-regulation of gene expression. Several examples of major metabolic DEGs are provided for each cluster. An annotated list of DEGs identified in each K-means cluster is provided in Additional file 1, which also includes a composite graph of all K-means clusters including the low-amplitude changes in Clusters 4 and 8, both of which were down-regulated with fasting and sharply up-regulated with refeeding

Back to article page