sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression.
IF: 17.906
Cited by: 7


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 , can be applied to learn biologically interpretable patterns of eQTL tissue-specificity and generate testable mechanistic hypotheses.


Gene Expression
Matrix factorization
Tissue-specific eQTLs
Transcription factors
Ubiquitous eQTLs

MeSH terms

Gene Expression Regulation
Models, Genetic
Quantitative Trait Loci
Transcription Factors


He, Yuan
Chhetri, Surya B
Arvanitis, Marios
Srinivasan, Kaushik
Aguet, François
Ardlie, Kristin G
Barbeira, Alvaro N
Bonazzola, Rodrigo
Im, Hae Kyung
Brown, Christopher D
Battle, Alexis

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