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Updated: Jan 27, 2026

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
Published on: October 3, 2025
Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically
Paul F Harrison1, Andrew D Pattison2, David R Powell3,2
1Monash Bioinformatics Platform, Monash University, Melbourne, Australia. Paul.harrison@monash.edu.
Abstract:
Differential gene expression analysis may discover a set of genes too large to easily investigate, so a means of ranking genes by biological interest level is desired. p values are frequently abused for this purpose. As an alternative, we propose a method of ranking by confidence bounds on the log fold change, based on the previously developed TREAT test. These confidence bounds provide guaranteed false discovery rate and false coverage-statement rate control. When applied to a breast cancer dataset, the top-ranked genes by Topconfects emphasize markedly different biological processes compared to the top-ranked genes by p value.
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