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 1 ; Yang, Peng 1 ; Zhang, Yongjin 2 ; Li, Qiaowei 1 ; Fan, Xinhao 1 ; Chen, Ruipu 1 ; Yan, Chao 1 ; Zeng, Mu 1 ; Yang, Yalan 1 ; Tang, Zhonglin 1 ;
作者机构： 1.Chinese Acad Agr Sci, Kunpeng Inst Modern Agr Foshan, Agr Genom Inst, Foshan 528225, Peoples R China
2.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Key Lab Livestock & Poultry Multi MARA,Shenzhen Br, Shenzhen 518124, Peoples R China
3.GuangXi Engn Ctr Resource Dev Bama Xiang Pig, Bama 547500, Peoples R China
4.Henan Univ, Sch Life Sci, Kaifeng 475004, Peoples R China
5.Shenzhen Res Inst Henan Univ, Shenzhen Res Inst, Shenzhen 518000, Peoples R China
6.Univ Coll Dublin, Sch Vet Med, Belfield D04V1W8, Dublin, Ireland
7.Foshan Univ, Key Lab Anim Mol Design & Precise Breeding, Guangdong Prov Key Lab Anim Mol Design & Precise B, Guangdong Higher Educ Inst,Sch Life Sci & Engn, Foshan 528225, Peoples R China
关键词： Pig; Multi-omics; Genome; Gene expression; Epigenetics; Database
期刊名称：GENOMICS PROTEOMICS & BIOINFORMATICS （ 影响因子：7.9； 五年影响因子：9.1 ）
ISSN： 1672-0229
年卷期： 2025 年 23 卷 1 期
页码：
收录情况： SCI
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.
- 相关文献
作者其他论文 更多>>
-
Trends in crop yield estimation via data assimilation based on multi-interdisciplinary analysis
作者：Cao, Hong;Zhao, Rongkun;Xia, Lang;Wu, Shangrong;Yang, Peng;Cao, Hong;Zhao, Rongkun;Xia, Lang;Wu, Shangrong;Yang, Peng
关键词：Yield simulation; Data assimilation; Remote sensing; Crop growth model; Crops
-
A Spectral Hierarchical Machine Learning for Predicting Arsenic Concentration in Farmland Soil Using Sentinel-2 Imagery
作者：Wang, Li;Wu, Shangrong;Xia, Lang;Zha, Yan;Yang, Peng;Wang, Li;Wu, Shangrong;Xia, Lang;Zha, Yan;Yang, Peng;Zhou, Yong;Zhou, Zehan
关键词：Soil; Metals; Predictive models; Feature extraction; Remote sensing; Biological system modeling; Radio frequency; Noise; Accuracy; Surfaces; Farmland soil; machine learning; multispectral image; soil arsenic; spectral hierarchization
-
DPImpute: A Genotype Imputation Framework for Ultra-Low Coverage Whole-Genome Sequencing and its Application in Genomic Selection
作者：Zheng, Weigang;Wang, Chao;Dong, Wenjun;Liu, Yuwen;Zheng, Weigang;Wang, Chao;Dong, Wenjun;Liu, Yuwen;Zheng, Weigang;Ma, Wenlong;Chen, Zhilong;Wang, Chao;Sun, Tao;Dong, Wenjun;Zhang, Song;Tang, Zhonglin;Li, Kui;Liu, Yuwen;Zheng, Weigang;Ma, Wenlong;Chen, Zhilong;Wang, Chao;Sun, Tao;Dong, Wenjun;Zhang, Song;Tang, Zhonglin;Li, Kui;Liu, Yuwen;Zhang, Wenjing;Tang, Zhonglin;Liu, Yuwen;Zhao, Yunxiang
关键词：breeding models; genetic screening of embryos; genomic selection; genotype imputation; single cell genotype
-
Iturin and fengycin lipopeptides inhibit pathogenic Fusarium by targeting multiple components of the cell membrane and their regulative effects in wheat
作者：Yuan, Qing-Song;Yang, Peng;Tabl, Karim M.;Guo, Mao-Wei;Zhang, Jing-Bo;Liao, Yu-Cai;He, Wei-Jie;Yuan, Qing-Song;Yang, Peng;Liu, Yi-Ke;Tabl, Karim M.;Guo, Mao-Wei;Wu, Ai-Bo;Huang, Tao
关键词：antagonism;
Fusarium graminearum ;Fusarium head blight; induced systemic resistance; iturin and fengycin lipopeptides; plant growth regulation -
Plasma-based ultrasensitive detection of Mycobacterium tuberculosis ESAT6/ CFP10 fusion antigen using a CRISPR-driven aptamer fluorescence testing (CRAFT)
作者：Liu, Siyuan;Xiao, Guohui;Xu, Yating;Tian, Lin;Zhang, Su;Zhang, Guoliang;Li, Peixuan;Fan, Xinhao;Li, Peixuan;Fan, Xinhao
关键词：Mycobacterium tuberculosis; Aptamer; ESAT6/CFP10; CRISPR; Plasma
-
Optimizing the landscape in grain production and identifying trade-offs between ecological benefits based on production possibility frontiers: A case study of Beijing-Tianjin-Hebei region
作者：Liu, Qinghua;Sun, Xiao;Huang, Qingxu;Huang, Qingxu;Qiao, Jianmin;Fang, Guangji;Wang, Chenrui;Sun, Jing;Yang, Peng;Ren, Yuhan
关键词：Production possibility frontiers; Trade-off; Landscape optimization; Grain production; Ecological benefits
-
Development and molecular cytogenetic identification of a new wheat-rye 6RL ditelosomic addition and 1R (1B) substitution line with powdery mildew resistance
作者：Han, Guohao;Wang, Jing;Yan, Hanwen;Cao, Lijun;Gu, Tiantian;Shi, Zhipeng;Liu, Hong;An, Diaoguo;Li, Xiuquan;Li, Lihui;Zhou, Yilin;Liu, Wei;An, Diaoguo
关键词：powdery mildew; common wheat; Triticale; 6RL ditelosomic addition line; agronomic performance; marker-assisted selection (MAS)
