PIGOME: An Integrated and Comprehensive Multi-omics Database for Pig Functional Genomics Studies.

Area of Science:

• Genomics
• Bioinformatics
• Animal Science

Background:

• Pigs are vital protein sources and crucial models for human development and disease research.
• Extensive high-throughput sequencing in pigs has generated vast data, but dedicated multi-omics databases remain limited.
• Functional genomics research in pigs requires integrated, accessible omics datasets.

Purpose of the Study:

• To introduce PIGOME, a comprehensive and user-friendly database for pig multi-omics data.
• To consolidate diverse omics datasets and associated metadata for enhanced pig functional genomics research.
• To provide tools for exploring gene expression, epigenetic patterns, and trait associations in pigs.

Main Methods:

• Compilation of seven types of pig omics datasets: WGS, RNA-seq, miRNA-seq, ChIP-seq, ATAC-seq, BS-seq, and MeRIP-seq.
• Integration of data from 6901 samples across 392 projects with curated metadata, gene annotation, and QTL information.
• Development of user-friendly 'Explore' and 'Browse' functions and visualization tools for genomic variants, gene expression, and epigenetic signals.

Main Results:

• PIGOME houses a substantial collection of pig multi-omics data with rich metadata.
• The database offers integrated gene annotation and quantitative trait locus (QTL) information.
• Visualization tools enable efficient exploration of spatiotemporal gene expression, epigenetic patterns, and regulatory mechanisms.

Conclusions:

• PIGOME serves as a valuable resource for advancing pig functional genomics and breeding strategies.
• The database facilitates research into pig development, diseases, and economic traits.
• PIGOME supports comparative genomics and human biomedical research by leveraging pig as a model organism.