Additional file 2 of Molecular characterization of breast cancer cell pools with normal or reduced ability to respond to progesterone: a study based on RNA-seq

Additional file 2: Supplementary Table 1. Differentially expressed (DE) genes (BH-adjusted P < 0.05) between vehicle treated T-47D control cells and P4-treated T-47D control cells. Three independent biological replicates per treatment/condition were sequenced. Supplementary Table 2. Differentially expressed (DE) genes (BH-adjusted P < 0.05) between vehicle-treated PR-low pools and P4-treated PR-low pools. Three independent biological replicates per treatment/condition were sequenced. Supplementary Table 3. Differentially expressed (DE) genes (BH-adjusted P < 0.05) between vehicle treated T-47D control cells and P4/E2-treated T-47D control cells. Three independent biological replicates per treatment/condition were sequenced. Supplementary Table 4. Differentially expressed (DE) genes (BH-adjusted P < 0.05) between vehicle-treated PR-low pools and P4/E2-treated PR-low pools. Three independent biological replicates per treatment/condition were sequenced. Supplementary Table 5. Differentially expressed (DE) genes (BH-adjusted P < 0.05) between vehicle-treated PR-low pools and vehicle treated T-47D control cells. Three independent biological replicates per treatment/condition were sequenced. Supplementary Table 6. Differentially expressed (DE) genes (BH-adjusted P < 0.05) between P4-treated PR-low pools and P4-treated T-47D control cells. Three independent biological replicates per treatment/condition were sequenced. Supplementary Table 7. Differentially expressed (DE) genes (BH-adjusted P < 0.05) between P4/E2-treated PR-low pools and P4/E2-treated T-47D control cells. Three independent biological replicates per treatment/condition were sequenced. Supplementary Table 8. Top 30 gene ontology (GO) biological processes, cellular components (CC) and molecular functions (MF) significantly enriched after P4/E2 treatment in control pools. Annotated = total number of expressed genes in the term; significant = number of genes with BH-adjusted P-value < 0.05 in the term. P-values are from a Fisher’s exact test run in TopGO using the weight01 algorithm to account for the GO hierarchy. Supplementary Table 9. Top 30 gene ontology (GO) biological processes, cellular components (CC) and molecular functions (MF) significantly enriched after P4/E2 treatment in PR-low pools. Annotated = total number of expressed genes in the term; significant = number of genes with BH-adjusted P-value < 0.05 in the term. P-values are from a Fisher’s exact test run in TopGO using the weight01 algorithm to account for the GO hierarchy. Supplementary Table 10. Top 30 gene ontology (GO) biological processes, cellular components (CC) and molecular functions (MF) significantly enriched among the 3′352 differentially expressed genes between P4/E2 treated control and PR-low pools. Annotated = total number of genes in the term; significant = number of genes with BH-adjusted P-value < 0.05 in the term. P-values are from a Fisher’s exact test run in TopGO using the weight01 algorithm to account for the GO hierarchy.