Pathway enrichment analysis in microarray gene-expression data.

Hypergeometric tests were performed using the clusterProfiler v3.16.0 package to calculate enrichment of Gene Ontology pathways (for example, cellular components, molecular functions and biological processes) in the microarray data. Genes significantly enriched or depleted in Ad/MF and P3 mSSCs compared with in adult mSSCs were defined on the basis of a log₂(fold change) value of >1 or <−1 and adjusted P < 0.01 (Benjamini–Hochberg procedure). Pathways were selected using the ‘enrichGO’ function with P < 0.01 and adjusted P < 0.05.

Geneset enrichment analysis (GSEA) was performed using the Broad Institute’s online software with a gene list ordered by log₂-fold enrichment in Ad/MF and P3 mSSCs compared with adult mSSCs. Only gene sets with a nominal P < 0.05 and false discovery rate < 0.25 were considered.