PigGTEx
PigGTEx maps genetic regulatory variants to transcriptomic phenotypes across pig tissues to characterize genetic regulation relevant to animal breeding and human biomedicine.
Key Features:
- Extensive Data Collection: Processed 9,530 RNA-sequencing samples and 1,602 whole-genome sequencing samples from pigs.
- Genotype Imputation Panel: A specialized pig genotype imputation panel was developed to facilitate genotype imputation across samples.
- Transcriptional Landscape Characterization: Characterized the transcriptional landscape across over 100 pig tissues.
- Association with Transcriptomic Phenotypes: Associated millions of genetic variants with five distinct types of transcriptomic phenotypes across 34 tissues.
- Genotype–Breed/Cell Type Interactions: Evaluates interactions between genotype and breed or cell type.
- Tissue-Specific Regulatory Effects: Assesses tissue specificity of regulatory effects across tissues.
- Multi-Omics Data Integration: Integrates multi-omics data to elucidate molecular mechanisms underlying genetic regulation.
Scientific Applications:
- Interpreting genetic associations in pigs: Links regulatory variants to approximately 80% of genetic associations for 207 complex phenotypes in pigs.
- Comparative and translational research: Reveals similarities between pig and human gene expression patterns and genetic regulation of complex phenotypes, supporting the use of pigs as a biomedical model.
Methodology:
Processed RNA-sequencing and whole-genome sequencing data, developed a pig genotype imputation panel, performed association analyses linking millions of variants to five transcriptomic phenotype types across 34 tissues, evaluated genotype–breed and genotype–cell type interactions, assessed tissue-specific regulatory effects, and integrated multi-omics data.
Topics
Details
- Cost:
- Free of charge
- Tool Type:
- web application
- Operating Systems:
- Mac, Linux, Windows
- Programming Languages:
- R, Python
- Added:
- 2/1/2023
- Last Updated:
- 11/24/2024
Operations
Publications
Fang L, Teng J, Gao Y, Yin H, Bai Z, Liu S, Zeng H, Bai L, Cai Z, Zhao B, Li X, Xu Z, Lin Q, Pan Z, Yang W, Yu X, Guan D, Hou Y, Keel B, Rohrer G, Lindholm-Perry A, Oliver W, Ballester M, Crespo-Piazuelo D, Quintanilla R, Canela-Xandri O, Rawlik K, Xia C, Yao Y, Zhao Q, Yao W, Yang L, Li H, Zhang H, Liao W, Chen T, Karlskov-Mortensen P, Fredholm M, Amills M, Clop A, Giuffra E, Wu J, Cai X, Diao S, Pan X, Wei C, Li J, Cheng H, Wang S, Su G, Sahana G, Lund M, Dekkers J, Kramer L, Tuggle C, Corbett R, Groenen MA, Madsen O, Gòdia M, Rocha D, Charles M, Li C, Pausch H, Hu X, Frantz L, Luo Y, Lin L, Zhou Z, Zhang Z, Chen Z, Cui L, Xiang R, Shen X, Li P, Huang R, Tang G, Li M, Zhao Y, Yi G, Tang Z, Jiang J, Zhao F, Yuan X, Liu X, Chen Y, Xu X, Zhao S, Zhao P, Haley C, Zhou H, Wang Q, Pan Y, Ding X, Ma L, Li J, Navarro P, Zhang Q, Li B, Tenesa A, Li K, Liu G, Zhang Z. A compendium of genetic regulatory effects across pig tissues. Unknown Journal. 2022. doi:10.21203/rs.3.rs-2261680/v1.