Fig. 3
From: Cis-acting super-enhancer lncRNAs as biomarkers to early-stage breast cancer
Expression of 27 potentially cis-acting SE-lncRNAs and their neighboring mRNA and 4 of the highest differentially expressed SE-lncRNAs in the MCF10A progression series. a Expression of 11 SE-lncRNAs and their neighboring mRNAs in progression that correlated in TANRIC. Top are upregulated SE-lncRNAs and their associated mRNA while bottom are down regulated and their associated mRNA. SE-lncRNA-mRNA pairs: FAM83H-AS1 and FAM83H, HOTAIR and HOXC11, CTD-2127H9.1 and OSMR, LINC01057 and SLC44A3, NR2F1-AS1 and NR2F1, HOXA11-AS and HOXA11, RP11-379F4.4 and RARRES1, KB-14601.5 and ZNF706, RP11-403A21.1 and LAMA3, RP3-483K16.4 and ELOVL5, SNHG18 and SEMA5A. b Expression of 16 SE-lncRNAs and their neighboring mRNAs in progression that did not correlate in TANRIC. Top are upregulated SE-lncRNAs and their associated mRNA, while bottom are down regulated and their associated mRNA. SE-lncRNA-mRNA pairs: CTD-2033D15.1 and THBS1, RP11-303E16.3 and CENPN, RP11-346D6.6 and DKK1, RP11-560J1.2 and JARID2, PCAT1 and FAM84B, RP11-61F12.1 and COTL1, RP11-57P1.4 and ADRM1, RP11-326G21.1 and PDE4DIP, RP11-620J15.3 and XRCC6BP1, LINC01125 and ACTR1B, HCG11 and BTN1A1, MIR22HG and WDR81, C4B-AS1 and C4B, CCND2-AS1 and CCND2, FAM13A-AS1 and FAM13A, RP11-137H2.6 and FAM213A. c Expression of the highest differentiated SE-lncRNAs in progression. Top two are upregulated SE-lncRNAs, while bottom two are down regulated. One-way ANOVA with Tukey correction was carried out to evaluate statistical significance of gene expression between cell lines, n = 3, * = P < 0.05, error bars represent standard deviation. Full statistical analysis is presented in Additional file 6: Table S3