Combination of UHPLC-MS/MS with context-specific network and cheminformatic approaches for identifying bioactivities and active components of propolis

•Combining LC-MS/MS and CODA/COCONUT predicted propolis-associated immune diseases.•Propolis displayed therapeutic effects against atopic dermatitis.•CODA/COCONUT provided compound-associated genes based on constituents of propolis.•Propolis regulated the expression of target genes predicted by the network analysis.•Active compounds of propolis and their combinatorial effects was discovered.