Related Experiment Video
Updated: Jan 23, 2026

A Protocol for Using Gene Set Enrichment Analysis to Identify the Appropriate Animal Model for Translational Research
Published on: August 16, 2017
Gene set enrichment for reproducible science: comparison of CERNO and eight other algorithms
Joanna Zyla1,2, Michal Marczyk1,3, Teresa Domaszewska2
1Data Mining Group, Faculty of Automatic Control, Electronic and Computer Science, Institute of Automatic Control, Silesian University of Technology, Gliwice, Poland.
Motivation:
Analysis of gene set (GS) enrichment is an essential part of functional omics studies. Here, we complement the established evaluation metrics of GS enrichment algorithms with a novel approach to assess the practical reproducibility of scientific results obtained from GS enrichment tests when applied to related data from different studies.
Results:
We evaluated eight established and one novel algorithm for reproducibility, sensitivity, prioritization, false positive rate and computational time. In addition to eight established algorithms, we also included Coincident Extreme Ranks in Numerical Observations (CERNO), a flexible and fast algorithm based on modified Fisher P-value integration. Using real-world datasets, we demonstrate that CERNO is robust to ranking metrics, as well as sample and GS size. CERNO had the highest reproducibility while remaining sensitive, specific and fast. In the overall ranking Pathway Analysis with Down-weighting of Overlapping Genes, CERNO and over-representation analysis performed best, while CERNO and GeneSetTest scored high in terms of reproducibility.
Availability And Implementation:
tmod package implementing the CERNO algorithm is available from CRAN (cran.r-project.org/web/packages/tmod/index.html) and an online implementation can be found at http://tmod.online/. The datasets analyzed in this study are widely available in the KEGGdzPathwaysGEO, KEGGandMetacoreDzPathwaysGEO R package and GEO repository.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Related Concept Videos
Psychology as a Science
The scientific method in psychology involves six critical steps: making observations, formulating hypotheses, conducting tests, analyzing...
Trial and Error and Algorithm
The Sense of Self: Reflected Self-Appraisal and Social Comparison
Overview of Biostatistics in Health Sciences
Gene Conversion
Multiple Comparison Tests
It would be easy to compare two samples using a significance alpha level of 0.05. In other words, there is only one sample pair to be compared. However, it would be difficult to identify a significantly different sample if the number...

