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Transcriptomes are routinely used to prioritize genes underlying specific phenotypes. Current approaches largely focus on differentially expressed genes (DEGs), despite the recognition that phenotypes emerge via a network of interactions between genes and proteins, many of which may not be differentially expressed. Furthermore, many practical applications lack sufficient samples or an appropriate control to robustly identify statistically significant DEGs.

PathExt: a general framework for path-based mining of omics-integrated biological networks