ArticleGenome biology2020
sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 32 citations in OpenAlex.
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- Decoding the dark genome reveals its organisation into modular disease networks.Scientific reports · 2026Article
- Sparse matrix factorization robust to sample sharing across GWASs reveals interpretable genetic components.American journal of human genetics · 2025Article
- Abundant repressor binding sites in human enhancers are associated with the fine-tuning of gene regulation.iScience · 2025Article
- Cross-tissue transcriptome-wide association identify novel T1D susceptibility genes and drug candidates.Frontiers in immunology · 2025Article
- ebnm: An R Package for Solving the Empirical Bayes Normal Means Problem Using a Variety of Prior Families.Journal of statistical software · 2025Article
- Integrative genomic analyses identify neuroblastoma risk genes involved in neuronal differentiation.Human genetics · 2024Article
- PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs.Genome biology · 2024Article
- A scalable approach to characterize pleiotropy across thousands of human diseases and complex traits using GWAS summary statistics.American journal of human genetics · 2023Article
- A Transcriptome-Wide Analysis of Psoriasis: Identifying the Potential Causal Genes and Drug Candidates.International journal of molecular sciences · 2023Article
- A scalable variational approach to characterize pleiotropic components across thousands of human diseases and complex traits using GWAS summary statistics.medRxiv : the preprint server for health sciences · 2023Article
- EEF1A1 transcription cofactor gene polymorphism is associated with muscle gene expression and residual feed intake in Nelore cattle.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Article
- Redefining tissue specificity of genetic regulation of gene expression in the presence of allelic heterogeneity.American journal of human genetics · 2022Article
- A compendium of uniformly processed human gene expression and splicing quantitative trait loci.Nature genetics · 2021Article
- sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression.Genome biology · 2020Article
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Authors and funding
12 authors at 4 institutions in 1 country.
Funding
Abstract
Genetic regulation of gene expression, revealed by expression quantitative trait loci (eQTLs), exhibits complex patterns of tissue-specific effects. Characterization of these patterns may allow us to better understand mechanisms of gene regulation and disease etiology. We develop a constrained matrix factorization model, sn-spMF, to learn patterns of tissue-sharing and apply it to 49 human tissues from the Genotype-Tissue Expression (GTEx) project. The learned factors reflect tissues with known biological similarity and identify transcription factors that may mediate tissue-specific effects. sn-spMF, available at https://github.com/heyuan7676/ts_eQTLs , can be applied to learn biologically interpretable patterns of eQTL tissue-specificity and generate testable mechanistic hypotheses.
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