Fig. 6: Differentially expressed and multifunctional genes in the CAKUT_sig1 module.

a For the CAKUT_sig1 module, the heatmap shows the expression landscape of significantly differentially expressed CNV-lncRNAs and protein coding genes (|log₂FoldChange | ≥ 4, P_adj < 0.05) in the developmental kidney, heart, brain and cerebellum (Kidney samples: n = 40, heart samples: n = 50, brain samples: n = 87, cerebellum samples: n = 27). The counts (including CNV-lncRNAs and protein coding genes) of differentially expressed genes in each cluster are shown on the left. The tissue types of corresponding samples are labeled above the heatmap. The colors represent gene expression value (log₁₀TPM) in different samples (Supplementary Data 13–15). b Functional annotations of heart, brain and cerebellum differentially expressed gene clusters compared to kidney samples are shown (Supplementary Data 13–15). For each gene cluster, the top seven biological process GO terms (ranked by P_adj) are shown. The x and y axes represent values of −log₁₀(P_adj) and GO terms, respectively. The red dashed line indicates P_adj of 0.05. The colors of the bars represent different gene clusters. c Functional annotations of kidney differentially expressed gene clusters compared to heart, brain and cerebellum samples are shown (Supplementary Data 13–15). For each gene cluster, organ development-associated functional annotations are shown. The associated organs of corresponding GO terms are labeled above the bar plot. The x and y axes represent GO terms and values of −log₁₀(P_adj), respectively. The red dashed line indicates P_adj of 0.05. The colors of the bars represent different gene clusters. d Gene counts and intersection of congenital heart disease (CHD), neurodevelopmental disorders (NDDs) and CAKUT gene sets are shown in Venn diagrams (Supplementary Data 16). Intersection counts are shown in red font. e Distribution of known CAKUT genes associated with two or more phylogenetic disorders (intersection in d, n = 32) in developmental WGCNA modules (Supplementary Table 3; Supplementary Data 16). f Expression patterns of CAKUT genes associated with extrarenal development defects in the CAKUT_sig1 module (n = 14) in different tissues are shown in the violin plots. The x and y axes represent tissue types and gene expression levels (log₂TPM), respectively (Supplementary Data 1, 16). CHD congenital heart disease, NDD neurodevelopmental disorders, CAKUT congenital anomalies of the kidney and urinary tracts.