Gene expression profiling of T47D cells stably expressing WT or SUMO-deficient PR, treated with or without R5020 for six hours. (A) Western blot showing total and phospho-Ser294 PR proteins (total ERK1/2 served as a loading control) in 12 human breast tumors. (B) T47D cells stably expressing either wild-type PR-B (WT), SUMO-deficient mutant K388R PR-B (KR), or empty vector (null) controls were treated without or with R5020 prior to western blotting for PR-B. (C) Heat map showing normalized expression values for differentially expressed transcripts (fold change > 8.0 in at least one sample, BH adjusted P < 0.001). Biological duplicates are shown for each treatment group and notable gene expression categories (numbered 1-4 on right side) are described (see Results). (D) Venn diagrams showing up- or down-regulated PR target genes following progestin treatment (log2 fold change > 0.6, BH adjusted P < 0.01; common fold change > 1.5). (E) Venn diagrams (as in part D) depicting the number of ligand-independent (LI) PR target genes up- or down-regulated relative to PR-null cells. (F) Relative mRNA expression (as determined by RT-qPCR) of selected PR target genes in T47D cells stably expressing vector control (PR-null), WT or KR PR and treated without or with R5020 for six hours; genes chosen from ligand-dependent (LD) or LI Venn categories are indicated (note matching color labels). Data are represented as mean of n = 3 +/- SD. [See also Additional file 5. BH, Benjamini and Hochberg; n, number; PR, progesterone receptor; SD, standard deviation; SUMO, small ubiquitin-like modifier.