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An increasing amount of evidence suggests that canonical pathways and standard molecular signature databases are incomplete and inadequate to model the complex behavior of cell physiology and pathology. Yet, many Gene Set Analysis (GSA) studies still rely on these databases to identify disease biomarkers and molecular mechanisms within a specific cell context. While tremendous effort has been invested in developing GSA tools, there is limited number of studies focusing on de novo assembly of context-specific gene sets as opposed to simply applying GSA using the standard gene set database.

Assembling cell context-specific gene sets: a case in cardiomyopathy