Gene set enrichment analyses (GSEAs) are widely used in genomic research to identify underlying biological mechanisms (defined by the gene sets), such as Gene Ontology terms and molecular pathways. There are two caveats in the currently available methods: (i) they are typically designed for group comparisons or regression analyses, which do not utilize temporal information efficiently in time-series of transcriptomics measurements, and (ii) genes overlapping in multiple molecular pathways are considered multiple times in hypothesis testing.