GTExVisualizer: a web platform for supporting ageing studies

• Published in: Bioinformatics (Oxford, England) Vol. 39; no. 5
• Main Authors: Guzzi, Pietro Hiram, Lomoio, Ugo, Veltri, Pierangelo
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 04.05.2023
• Subjects: Algorithms; Applications Note; Gene Expression Profiling; Humans; Software
• ISSN: 1367-4811; 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/btad303

Abstract Motivation Studying ageing effects on molecules is an important new topic for life science. To perform such studies, the need for data, models, algorithms, and tools arises to elucidate molecular mechanisms. GTEx (standing for Genotype-Tissue Expression) portal is a web-based data source allowing to retrieve patients’ transcriptomics data annotated with tissues, gender, and age information. It represents the more complete data sources for ageing effects studies. Nevertheless, it lacks functionalities to query data at the sex/age level, as well as tools for protein interaction studies, thereby limiting ageing studies. As a result, users need to download query results to proceed to further analysis, such as retrieving the expression of a given gene on different age (or sex) classes in many tissues. Results We present the GTExVisualizer, a platform to query and analyse GTEx data. This tool contains a web interface able to: (i) graphically represent and study query results; (ii) analyse genes using sex/age expression patterns, also integrated with network-based modules; and (iii) report results as plot-based representation as well as (gene) networks. Finally, it allows the user to obtain basic statistics which evidence differences in gene expression among sex/age groups. Conclusion The GTExVisualizer novelty consists in providing a tool for studying ageing/sex-related effects on molecular processes. Availability and implementation GTExVisualizer is available at: http://gtexvisualizer.herokuapp.com. The source code and data are available at: https://github.com/UgoLomoio/gtex_visualizer.