Fig. 4: daf-18(yh1) is a hypomorphic allele that differentially affects gene expression in daf-2(−) mutants.
a A principal component (PC) analysis showing relative distance among samples. b Two comparisons for subsequent analyses of RNA-seq data [red: daf-2(−) vs. daf-2(−); daf-18(yh1), purple: daf-2(−) vs. daf-2(−); daf-18(−)]. c, d Overlaps between genes upregulated (c) and downregulated (d) in daf-2(−) mutants compared to daf-2(−); daf-18(−) or daf-2(−); daf-18(yh1) mutants (p values were calculated by using exact hypergeometric probability test. RF: representation factor). e, f Comparisons of the extent of gene expression changes between the two comparisons. Genes whose expression was upregulated (e) and downregulated (f) in daf-2(−) mutants compared to daf-2(−); daf-18(−) mutants were considered. Overlaps between purple and red bars were marked in yellow. g A scatter plot showing the effects of daf-18(−) and daf-18(yh1) mutations on gene expression in daf-2(−) mutants. Shown are genes whose expression levels were specifically upregulated (red dot: 118 genes) or downregulated (blue dot: 219 genes) in daf-2(−) animals compared with daf-2(−); daf-18(−) worms (fold change > 2, Benjamini and Hochberg (BH)-adjusted p value < 0.05), but were only slightly altered compared with daf-2(−); daf-18(yh1) animals (fold change < 2 relative to daf-18(−)) in daf-2(−) mutants. See Supplementary Fig. 4 h, i, l, m for gene ontology and tissue enrichment analysis results of these genes. h, i Confirmation of the expression changes of the top 50-ranked genes in (g) by using quantitative RT-PCR. Both axes are log2-transformed. See Supplementary Fig. 5 and Supplementary Dataset 1 for details.
