Fig. 6: The transcriptome of KDM5A-KO cells.

A Hierarchical clustering of gene expression profiles from 3 biologically independent samples based on Pearson correlation coefficient in WT and KDM5A-KO cells. Colors from green to red indicate weak-to- strong correlation. WT: wild type, 143B cell line. B Volcano plot of all genes analyzed in the present study. Blue, significantly differently downregulation genes. Red, significantly differently overregulation genes. Black, nonsignificantly differently expressed genes (DEG). C, D GO analysis of upregulated (C) and downregulated genes (D) for biological processes in KDM5A-KO cells. E The genes that were involved in >4 pathways of enrichment sets, including IL6 (shared by eight pathways), TNFAIP3 (shared by six pathways), IL15 and INHBA (shared by five pathways), CCL2, ICMA1, IL1B, IL7, IRF7, ITGB3, LIF, and MMP14 (shared by four pathways). All core enrichment genes in the 13 enriched sets were shown in Supplementary Table S1. F A protein–protein interaction (PPI) network of the 12 enrichment genes was constructed by using the STRING online database (https://string-db.org/). G The expression of the enrichment genes in KDM5A-KO cells was detected using RT-qPCR analyses. Data were shown as the mean ± S.D (n = 3). *p < 0.05, **p < 0.01, ***p < 0.01.