Enrichment Analysis of Transcriptomic and Proteomic Data

For bulk RNA-seq data, GSEA was performed based on genes ranked in order of log₂FC and the functional WikiPathways (www.wikipathways.org) database via WEB-based GEne SeT AnaLysis Toolkit (WebGestalt) (70 (link)). Only significant (FDR < 0.05) pathway categories with 10 to 500 genes were considered for enrichment analyses. For proteomics and integrated transcriptomic-proteomic datasets, enrichment analysis was performed based on significant DEGs/DEPs (|log₂FC| > 1, adjusted P < 0.05) in Metacore (Metacore/">https://clarivate.com/products/Metacore/; Clarivate Analytics, London, UK). Only significant (FDR < 0.05) prebuilt process networks were presented. Up-regulated and down-regulated process networks are shown using −log₁₀(FDR) and log₁₀(FDR), respectively. For bulk RNA-seq data comparison between Pax7-nGFP⁺ iMPCs and Pax7-nGFP⁺ myoblasts, ORA was performed using the R package goseq v1.42.