Bringing public health to the forefront in gene set enrichment analysis

Gene set enrichment analysis is integral to the study of genomics, allowing researchers to interpret data collected at the level of single genes by their collective involvement in biological pathways. However, the assessment and comparison of such methods has been generally ad hoc and lacking in data related to public health.

In a paper published recently in the journal Briefings in Bioinformatics, Ludwig Geistlinger, an investigator with the CUNY Institute for Implementation Science in Public Health and CUNY SPH Associate Professor Levi Waldron provided the most thorough benchmarking of gene set enrichment analysis methods to date, along with open-source software and extensive curated databases for applying these benchmarks to new gene set enrichment methods.

“While most benchmarking studies of gene set enrichment analysis have employed simulations and a couple datasets on model organisms, our work incorporates a curated compendium of 75 expression datasets investigating 42 human diseases that have gene pathways of known relevance,” says Geistlinger, the study’s lead author. “This study improves our understanding of how gene set enrichment analysis methods perform in biomedical applications, and will help future developments focus on improvements relevant to public health. We wanted to provide specific advice to researchers about currently popular methods, but also to provide an easy-to-use framework for others to extend our efforts.”

About the Institute for Implementation Science in Population Health at the City University of New York
The CUNY Institute for Implementation Science in Population Health (ISPH) was founded on the notion that substantial improvements in population health can be efficiently achieved through better implementation of existing strategies, policies, and interventions across multiple sectors. We study how to translate and scale-up evidence-based interventions and policies within clinical and community settings in order to improve population health and reduce health disparities. CUNY ISPH. Pursuing population health gains through better implementation. Follow us on Twitter: @CUNYISPH.

About the CUNY Graduate School of Public Health and Health Policy
The CUNY Graduate School of Public Health and Health Policy (CUNY SPH) is committed to teaching, research and service that creates a healthier New York City and helps promote equitable, efficient and evidence-based solutions to pressing health problems facing cities around the world. For more information, visit

“Toward a gold standard for benchmarking gene set enrichment analysis,” Ludwig Geistlinger, Gergely Csaba, Mara Santarelli, Marcel Ramos, Lucas Schiffer, Nitesh Turaga, Charity Law, Sean Davis, Vincent Carey, Martin Morgan, Ralf Zimmer, Levi Waldron, Briefings in Bioinformatics, February 2020, bbz158,