Extended Data Fig. 5: Transcriptome gene-expression profiling in experiments performed with different genetic backgrounds and tissues.

Transcriptome gene-expression profiling in experiments performed with different genetic backgrounds and tissues. a, Twenty cotyledons and fifty hypocotyls were sampled for RNA-seq. b, The two major principal components (PC) from a PC analysis of the log₂(FPKM + 1)-transformed gene expression levels in the different samples. c and d, The number of significantly up- and downregulated genes in the cotyledons (c) and hypocotyls (d) of pif4 and cdfq mutants relative to the wild type. e and f, The number of genes showing the same and opposite directions of regulation in the cotyledon (e) and hypocotyls (f) of pif4 and cdfq mutants relative to the wild type. A hypergeometric test showed that the probability of the overlap between the differentially expressed genes (DEGs) in pif4 and cdfq for cotyledons and hypocotyls was 4.882719e-74 and 0, respectively, indicating that the difference in the expression level of genes in these transcriptomes is higher than expected by chance. g, Overlapping gene set between CDF2 targets and DEGs in the cdfq mutant relative to the wild type. h, Overlapping gene set between PIF4 targets and differentially expressed genes in the pif4 mutant relative to the wild type.