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Updated: Aug 16, 2026

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
Published on: October 3, 2025
Tests for differentiation in gene expression using a data-driven order or weights for hypotheses
Gerhard Hommel1, Siegfried Kropf
1Institut für Medizinische Biometrie, Epidemiologie und Informatik, Universität Mainz, Germany. hommel@imbei.uni-mainz.de
Abstract:
In the analysis of gene expression by microarrays there are usually few subjects, but high-dimensional data. By means of techniques, such as the theory of spherical tests or with suitable permutation tests, it is possible to sort the endpoints or to give weights to them according to specific criteria determined by the data while controlling the multiple type I error rate. The procedures developed so far are based on a sequential analysis of weighted p-values (corresponding to the endpoints), including the most extreme situation of weighting leading to a complete order of p-values. When the data for the endpoints have approximately equal variances, these procedures show good power properties. In this paper, we consider an alternative procedure, which is based on completely sorting the endpoints, but smoothed in the sense that some perturbations in the sequence of the p-values are allowed. The procedure is relatively easy to perform, but has high power under the same restrictions as for the weight-based procedures.
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