Extended Data Fig. 6: Regulation of Foxk1 and Foxk2 at the transcriptome and proteome levels.

a, Correlation between expression profiles of 3T3-L1 adipocytes overexpressing or knocked down for FOXK1 or FOXK2. x- and y-axes denote log₂-transformed expression in RPKM (reads per kilobase of transcript per million). The correlation and P values are derived from Pearson’s correlation test. Precise P values are presented from Pearson’s correlation tests. b, c, Overlaps (b) between genes upregulated and downregulated by FOXK1 and FOXK2 knockdown (left) and overexpression (right) profiles and heat maps (c) showing logFC values of overlapping genes from FOXK1 and FOXK2 knockdown (left) and overexpression (right) profiles. d, Commonly deregulated genes or proteins from RNA-seq (FOXK1, n = 3 and FOXK2, n = 2) and proteome (FOXK1, n = 4 and FOXK2, n = 2) profiles of knockdown and overexpression. The P values for overlaps were calculated using hypergeometric test by assuming all expressed protein-coding genes from this study as background (n = 17,038). e, f, Gene enrichment (biological process) analysis of commonly deregulated genes from FOXK1 and FOXK2 overexpression or knockdown in RNA-seq profiles (e) and proteome profiles (f). Axes denote –log₁₀P from the GeneSCF tool. The Fisher’s exact test P values obtained using GeneSCF functional enrichment tool. g, Regulation of glycolytic pathway genes or proteins in RNA-seq and proteome profiles. RNA-seq data for overexpression or knockdown experiments depicted here were performed and analysed in three biological replicas (FOXK1, n = 3) or two biological replicas (FOXK2, n = 2). Proteomics data for overexpression or knockdown experiments depicted here were performed and analysed in four biological replicas (FOXK1, n = 4) or two biological replicas (FOXK2, n = 2).