Figure 1
Volcano plots illustrating the differentially expressed mRNAs of BC and pre-ranked GSEA of BC patients comparing Survivors and Early recurrence. (A) Mid recurrence; (B) and Late recurrence; (C) in TCGA BC cohort. Primary BCs with cancer recurrence data were analyzed and categorized as follows: recurrence ≤2 years (Early), recurrence between 2–5 years (Mid), recurrence >5 years (Late), and no recurrence >5 years (Survivors). Left panels: In volcano plots, X-axes: log2 FC; Y-axes: −log 10 P-value from limma analysis. mRNAs with P-value < 0.05 and FC >1.5 are marked in red, with P-value < 0.05 and FC <1/1.5 in green, all others in black. Right panels: In pre-ranked GSEA, blue bar shows NES and red dots show –log10 FDR q-value. We only considered gene sets significantly enriched that met a threshold of NES >1.5 or <−1.5 and FDR q-value < 0.01. Abbreviations: BC, breast cancer; GESA, Gene Set Enrichment Analyses; TCGA, The Cancer Genome Atlas; FC, fold change; NES, normalized enrichment score; FDR, false discovery rate.
