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Literature DB >> 35115012

Comparison of confound adjustment methods in the construction of gene co-expression networks.

Alanna C Cote^1,2,3, Hannah E Young^1,2,3, Laura M Huckins^4,5,6,7,8,9.

Abstract

Adjustment for confounding sources of expression variation is an important preprocessing step in large gene expression studies, but the effect of confound adjustment on co-expression network analysis has not been well-characterized. Here, we demonstrate that the choice of confound adjustment method can have a considerable effect on the architecture of the resulting co-expression network. We compare standard and alternative confound adjustment methods and provide recommendations for their use in the construction of gene co-expression networks from bulk tissue RNA-seq datasets.

Entities: Chemical

Keywords: Batch effects; Co-expression; Complex traits; Confound; Covariate; Module discovery; Normalization; RNA-seq

Mesh：

Year: 2022 PMID： 35115012 PMCID： PMC8812044 DOI： 10.1186/s13059-022-02606-0

Source DB: PubMed Journal: Genome Biol ISSN： 1474-7596 Impact factor: 17.906

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