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Interpreting and visualizing pathway analyses using embedding representations with PAVER



William G Ryan V1, Ali Sajid Imami1, Hunter Eby1, John Vergis1, Xiaolu Zhang2, Jarek Meller3,4,5,6, Rammohan Shukla7 & Robert McCullumsmith1,8,9,*



1Department of Neurosciences, College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA; 2Department of Microbiology and Immunology, Louisiana State University Health Sciences Center, Shreveport, LA, USA; 3Department of Environmental and Public Health Sciences, University of Cincinnati, Cincinnati, OH, USA; 4Department of Computer Science, University of Cincinnati, Cincinnati, OH, USA; 5Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH, USA; 6Department of Informatics, Nicolaus Copernicus University, Toruń, Poland; 7Department of Zoology & Physiology, College of Agriculture, Life Sciences and Natural Resources, University of Wyoming, Laramie, WY, USA; 8Neurosciences Institute, ProMedica, Toledo, OH, USA; 9Department of Psychiatry, College of Medicine and Life Sciences, University of Toledo, Toledo, OH, USA; *Corresponding author



William G Ryan V - E-mail: William.Ryan2@rockets.utoledo.edu

Ali Sajid Imami - E-mail: Ali.Imami@rockets.utoledo.edu

Hunter Eby - E-mail: Hunter.Eby@rockets.utoledo.edu

John Vergis - E-mail: John.Vergis@utoledo.edu

Xiaolu Zhang - E-mail: xiaolu.zhang@lsuhs.edu

Jarek Meller - E-mail: mellerj@ucmail.uc.edu

Rammohan Shukla - E-mail: rshukla@uwyo.edu

Robert McCullumsmith - E-mail: robert.mccullumsmith@utoledo.edu; Phone: +1 205-789-0841 Fax: +1 419-383-3008


Article Type

Research Article



Received June 1, 2024; Revised July 4, 2024; July 4, 2024, Published July 4, 2024



Omics studies use large-scale high-throughput data to explain changes underlying different traits or conditions. However, omics analysis often results in long lists of pathways that are difficult to interpret. Therefore, it is of interest to describe a tool named PAVER (Pathway Analysis Visualization with Embedding Representations) for large scale genomic analysis. PAVER curates similar pathways into groups, identifies the pathway most representative of each group, and provides publication-ready intuitive visualizations. PAVER clusters pathways defined by their vector embedding representations and then identifies the term most cosine similar to its respective cluster’s average embedding. PAVER can integrate multiple pathway analyses, highlight relevant biological insights, and work with any pathway database.



Biocuration, computational biology, gene expression profiling, R, systems biology, pathway analysis




Ryan et al. Bioinformation 20(7): 700-704 (2024)


Edited by

P Kangueane






Biomedical Informatics



This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.