Ensembl transcript IDs of differentially expressed genes were imported in MetaCore (v6.32) and processed using the “enrichment analysis” workflow. For each time point (day 3 or day 14), all the up-regulated (FDR < 0.05), all the down-regulated (FDR < 0.05), and the top 2000 differentially expressed genes (FDR < 0.05) were analyzed. Each list was compared to a defined background set of genes consisting of all the expressed transcripts (FPKM > 1) at the relevant time point (day 3 or day 14). The “pathway maps” or “process networks” that were enriched in each analysis were considered significant when FDR < 0.05.

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