Comparison of the 32 surveyed methods in terms of the supported omics types, meta-analysis, embedded pathways databases and mapping unit. The majority of these methods can integrate transcriptomic data with genomic, epigenomic, proteomic and metabolomic data. Among these, 19 methods are capable of performing meta-analysis (multi-cohort analysis). Further, 22 have embedded databases and thus allow users to analyze their data without the need of providing pathway/gene set information. Most methods also automatically map the gene/compound IDs of the expression data to the gene/compound IDs presented in the pathways. The column ‘Inter. Visual.’ indicates whether the tool has an interactive interface. Six methods provide interactive pathway diagram that allow users to interactively explore the results and inspect the statistics obtained in each omics analysis