KnockRBP: an integrated multi-omics database of functional perturbation profiles for RNA-binding proteins

RNA-binding proteins (RBPs) regulate diverse post-transcriptional processes, yet their functional impacts across multiple molecular layers remain incompletely characterized. KnockRBP (https://knockrbp.xu-bioinfo.com) is presented as a comprehensive, multi-omics database systematically cataloging regulatory changes resulting from genetic perturbation of RBPs. The resource integrates 1453 datasets from GEO, ENA, and ENCORE, encompassing RNA-seq, Ribo-seq, microRNA (miRNA)-seq, and 3'RACE-seq across 639 RBPs, 182 cell lines, and 61 diseases. Regulatory outcomes covered include alternative splicing, alternative polyadenylation, RNA editing, transcript abundance, translation efficiency, and miRNA expression, with all events processed through standardized analytical pipelines and annotated with open reading frame consequences, predicted loss-of-function impacts, and established disease or drug associations. The web interface supports dataset browsing, RBP- and gene-centric multi-omics exploration, transcript structure visualization, and interactive regulatory network navigation, while integrated analytical modules enable prioritization of perturbation-responsive events, cross-layer regulatory inference, and evaluation of clinical relevance. In contrast to existing RBP resources, KnockRBP integrates multi-omics data with perturbation-aware functional annotation, enabling mechanistic investigation and identification of RBP-affected genes and events in post-transcriptional regulation. The database is freely accessible and intended for long-term maintenance, serving as a community resource to advance functional genomics research on RBPs and their roles in human disease.