数字农科院2.0

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

文献类型： 外文期刊

作者： Han, Guohao;Yang, Peng;Zhang, Yongjin;Li, Qiaowei;Fan, Xinhao;Chen, Ruipu;Yan, Chao;Zeng, Mu;Yang, Yalan;Tang, Zhonglin

作者机构：

关键词： （1-1-2）Pig;Multi-omics;Genome;Gene expression;Epigenetics;Database

期刊名称： GENOMICS PROTEOMICS & BIOINFORMATICS

ISSN： 1672-0229

年卷期： 2025 年 23 卷 1 期

页码：

收录情况： SCIE（2025版） ; ; CSCD（2025-2026年度） ; ; 科技核心（2024版）

摘要： In addition to being a major source of animal protein, pigs are an important model for studying development and diseases in humans. Over the past two decades, thousands of high-throughput sequencing studies in pigs have been performed using a variety of tissues from different breeds and developmental stages. However, multi-omics databases specifically designed for pig functional genomics research are still limited. Here, we present PIGOME, a user-friendly database of pig multi-omes. PIGOME currently contains seven types of pig omics datasets, including whole-genome sequencing (WGS), RNA sequencing (RNA-seq), microRNA sequencing (miRNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), assay for transposase-accessible chromatin sequencing (ATAC-seq), bisulfite sequencing (BS-seq), and methylated RNA immunoprecipitation sequencing (MeRIP-seq), from 6901 samples and 392 projects with manually curated metadata, integrated gene annotation, and quantitative trait locus information. Furthermore, various Explore and Browse functions have been established to provide user-friendly access to omics information. PIGOME implements several tools to visualize genomic variants, gene expression, and epigenetic signals of a given gene in the pig genome, enabling efficient exploration of spatiotemporal gene expression/epigenetic patterns, functions, regulatory mechanisms, and associated economic traits. Collectively, PIGOME provides valuable resources for pig breeding and is helpful for human biomedical research. PIGOME is available at https://pigome.com.

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