Galbase: a comprehensive repository for integrating chicken multi-omics data

文献类型： 外文期刊

第一作者： Fu, Weiwei

作者： Fu, Weiwei;Wang, Rui;Xu, Naiyi;Wang, Jinxin;Li, Ran;Asadollahpour Nanaei, Hojjat;Jiang, Yu;Nie, Qinghua;Zhao, Xin;Han, Jianlin;Han, Jianlin;Yang, Ning;Yang, Ning;Jiang, Yu

作者机构：

关键词： Chicken; Omics data; Complex traits; Database

期刊名称：BMC GENOMICS （ 影响因子：4.547； 五年影响因子：4.931 ）

ISSN： 1471-2164

年卷期： 2022 年 23 卷 1 期

页码：

收录情况： SCI

摘要： Background: Multi-omics data can provide a stereoscopic view to explore potential causal variations and genes, as well as underlying genetic mechanisms of complex traits. However, for many non-mammalian species, including chickens, these resources are poorly integrated and reused, greatly limiting genetic research and breeding processes of the species. Results: Here, we constructed Galbase, an easily accessible repository that integrates public chicken multi-omics data from 928 re-sequenced genomes, 429 transcriptomes, 379 epigenomes, 15,275 QTL entries, and 7,526 associations. A total of 21.67 million SNPs, 2.71 million InDels, and 488,583 cis-regulatory elements were included. Galbase allows users to retrieve genomic variations in geographical maps, gene expression profiling in heatmaps, and epigenomic signals in peak patterns. It also provides modules for batch annotation of genes, regions, and loci based on multi-layered omics data. Additionally, a series of convenient tools, including the UCSC Genome Browser, WashU Epigenome Browser, BLAT, BLAST, and LiftOver, were also integrated to facilitate search, visualization, and analysis of sequence features. Conclusion: Galbase grants new opportunities to research communities to undertake in-depth functional genomic studies on chicken. All features of Galbase make it a useful resource to identify genetic variations responsible for chicken complex traits.

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