Fig. 5
From: Modeling and analysis of Hi-C data by HiSIF identifies characteristic promoter-distal loops
The genes with gained PDLs in MCF7-TamR cells. a-c Experimental validation on the selected gained looping events in MCF7-TamR cells by 3C-qPCR and RT-qPCR. Left top panel: illustration of primers applied in 3C-qPCR experiments. Left bottom panel: 3C-qPCR. Right panel: RT-qPCR. TSS: transcription start site. GAPDH was used as the control for both relative interaction frequencies and relative gene expression. *p < 0.05 (two-sided t test). Error bars represent standard error of the mean (S.E.M.) with three experiments. Detected genes: a ACP1, b HECTD1, c MBIP. d Signaling pathway networks of the core components of three signaling pathways: ECM receptor interaction, regulation of actin cytoskeleton and focal adhesion enriched by GSEA with the upregulated genes of gained PLDs in MCF7-TamR cells. e Relapse-free survival analysis of CD9 mRNA levels in ERα + patients receiving only Tamoxifen but without chemotherapy. The patients (n = 670) were stratified by mRNA levels at the top quartile (25%) vs. the rest (75%). p value was determined by the log-rank test. Analysis was referred to the published paper [34]. HR, hazard ratio. f Same analysis of CD9 mRNA levels in ERα + patients without endocrine treatment (n = 500)