PIGOME

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-omics. 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.猪不仅是动物蛋白的重要来源，同时也是研究人类发育与疾病的关键模式动物。过去二十余年间，科研人员已利用不同品种、不同发育阶段猪的多种组织，开展了数千项高通量测序研究。然而，专门针对猪功能基因组学研究的多组学数据库仍相对稀缺。为此，我们推出了PIGOME——一款用户友好型猪多组学数据库。目前，PIGOME收录了来自6901个样本、392个项目的7类猪多组学数据集，涵盖全基因组测序（whole-genome sequencing, WGS）、RNA测序（RNA sequencing, RNA-seq）、微小RNA测序（microRNA sequencing, miRNA-seq）、染色质免疫沉淀测序（chromatin immunoprecipitation sequencing, ChIP-seq）、转座酶可及性染色质测序（assay for transposase-accessible chromatin sequencing, ATAC-seq）、亚硫酸氢盐测序（bisulfite sequencing, BS-seq）以及甲基化RNA免疫沉淀测序（methylated RNA immunoprecipitation sequencing, MeRIP-seq），并附带人工整理的元数据、整合的基因注释与数量性状位点（quantitative trait locus, QTL）信息。此外，该数据库还设置了多种“探索”与“浏览”功能，为用户提供便捷的多组学信息获取途径。PIGOME集成了多款分析工具，可可视化猪基因组中特定基因的基因组变异、基因表达与表观遗传信号，助力研究者高效探究基因的时空表达/表观遗传模式、生物学功能、调控机制以及相关经济性状。综上，PIGOME为猪育种工作提供了宝贵的研究资源，同时也对人类生物医学研究具有重要的辅助价值。

搜集汇总

背景与挑战

背景概述

PIGOME是一个专注于猪功能基因组学的多组学数据库，整合了七种数据类型，涵盖近7000个样本，涉及多种品种、组织和发育阶段。该数据库提供用户友好的界面，用于搜索和探索基因变异、表达及表观遗传信息，为猪育种和生物医学研究提供重要资源。