Clusterings and heat maps were performed on unlabeled data using “dist” and “hclust” functions in R, using Euclidean distance and the Ward agglomeration method. Analysis for enriched GO terms, KEGG pathways, and REACTOME pathways were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) Functional Annotation Tool (v6.8). GO terms and pathways were considered enriched if the fold enrichment is ≥2.0, the uncorrected P value is ≤0.05, and the minimum number of regulated genes in the pathway/term is ≥2.0. Analysis was performed three times using all regulated genes, using up-regulated genes, and using down-regulated genes only. The union of these three analyses was performed to provide a single list of results. Analysis for transcription factors was performed using orthologous genes between the mouse and the human with the DAVID Functional Annotation Tool (v6.8). Orthologous genes are aggregated in FAST DB from Ensembl Compara. The same thresholds and methods as GO terms and pathway analysis were used but with human data.

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