sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression.

IF: 17.906

Cited by: 14

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.

Keywords

Gene Expression

Matrix factorization

Tissue-specific eQTLs

Transcription factors

Ubiquitous eQTLs

MeSH terms

Gene Expression Regulation

Humans

Models, Genetic

Quantitative Trait Loci

Transcription Factors

Authors

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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