Logic-based analysis of gene expression data predicts association between TNF, TGFB1 and EGF pathways in basal-like breast cancer

•Pathway Logic is a rewriting-logic-based system for modeling biological pathways.•We propose a novel framework to integrate Pathway Logic and gene expression data.•TCGA dataset was analyzed to explain differences in breast cancer subtypes.•Our system detected subtype-specific paths from key receptors to transcription factors.