It has been increasingly accepted that
microRNA (
miRNA) can both activate and suppress gene expression, directly or indirectly, under particular circumstances. Yet, a systematic study on the switch in their interaction pattern between activation and suppression and between normal and
cancer conditions based on multi-omics evidences is not available. We built miRactDB, a database for
miRNA-gene interaction, at https://ccsm.uth.edu/miRactDB, to provide a versatile resource and platform for annotation and interpretation of
miRNA-gene relations. We conducted a comprehensive investigation on
miRNA-gene interactions and their biological implications across tissue types in both tumour and normal conditions, based on TCGA, CCLE and GTEx databases. We particularly explored the genetic and epigenetic mechanisms potentially contributing to the positive correlation, including identification of
miRNA binding sites in the gene coding sequence (CDS) and promoter regions of partner genes. Integrative analysis based on this resource revealed that top-ranked genes derived from TCGA tumour and adjacent normal samples share an overwhelming part of biological processes, which are quite different than those from CCLE and GTEx. The most active
miRNAs predicted to target CDS and promoter regions are largely overlapped. These findings corroborate that adjacent normal tissues might have undergone significant molecular transformations towards
oncogenesis before phenotypic and histological change; and there probably exists a small yet critical set of
miRNAs that profoundly influence various
cancer hallmark processes. miRactDB provides a unique resource for the
cancer and genomics communities to screen, prioritize and rationalize their candidates of
miRNA-gene interactions, in both normal and
cancer scenarios.