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. 2020 Jan 31;21:109. doi: 10.1186/s12864-020-6525-0

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© The Author(s). 2020

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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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