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

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...

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Bibliographic Details
Published in:Genome Biology 2022-02, Vol.23 (1), p.44-13, Article 44
Main Authors: Cote, Alanna C, Young, Hannah E, Huckins, Laura M
Format: Article
Language:English
Subjects:
Batch effects
Binding sites
Co-expression
Confound
Consortia
Covariate
Datasets
Gene expression
Gene Expression Profiling - methods
Gene Regulatory Networks
Methods
Normalization
Performance evaluation
RNA-Seq
Short Report
Transcription factors
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Summary: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.
ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-022-02606-0