Pig Matrix: a matched multi-omics 3D regulatory genomics database for evolutionary and comparative analyses in pigs

Abstract The pig (Sus scrofa) is an important model for evolutionary, comparative, and translational research, however, current functional genomic resources in pigs remain largely limited to one-dimensional genomic annotation and are therefore insufficient for systematically resolving regulatory region–gene relationships, particularly distal ones. Here, we present the Pig Matrix database, a comprehensive 3D regulatory genomics database for pigs, available at https://pigmatrix.kiz.ac.cn/. Built on a standardized experimental framework, Pig Matrix integrates matched multi-omics datasets across tissues, developmental stages, and porcine cell lines, including genomic, transcriptomic, epigenomic, and 3D genome information. In total, it contains 16 library types across 7 omics layers and 7,959 processed files from 1,170 libraries. By integrating epigenomic and 3D genome information, Pig Matrix links cis-regulatory elements to putative proximal and distal target genes, thereby facilitating interpretation of non-coding variants and genomic signals. This database provides modules for genes, candidate cis-regulatory elements, 3D genome architecture, genome browsing, and single cell transcriptomics, together with dedicated Evolution and Comparative resources and user-oriented Genome Annotation and LiftOver tools. A representative use case illustrates how 3D regulatory annotation extends interpretation beyond linear annotation alone, recovering additional candidate genes in domestication-related signals, notably including the classical domestication gene KIT. Pig Matrix also incorporates xenotransplantation-related resources and may support benchmarking of AI models for regulatory genomics. Together, Pig Matrix provides an integrated platform for regulatory interpretation, evolutionary analysis, and comparative genomics in pigs.