Title
Interpreting and visualizing pathway analyses using embedding representations with PAVER
Authors
William G Ryan V1, Ali Sajid Imami1, Hunter Eby1, John Vergis1, Xiaolu Zhang2, Jarek Meller3,4,5,6, Rammohan Shukla7 & Robert McCullumsmith1,8,9,*
Affiliation
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
Date
Received June 1, 2024; Revised July 4, 2024; July 4, 2024, Published July 4, 2024
Abstract
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.
Keywords
Biocuration, computational biology, gene expression profiling, R, systems biology, pathway analysis
Citation
Ryan et al. Bioinformation 20(7): 700-704 (2024)
Edited by
P Kangueane
ISSN
0973-2063
Publisher
License
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.
