GTExVisualizer: a web platform for supporting ageing studies

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; (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 GTExVisualizer is available at : http://gtexvisualizer.herokuapp.com. The source code is available at: https://github.com/UgoLomoio/gtex_visualizer

Focusing on Gender and Age Information as Lens for Gene Expression Data: Application to Dyslipidemia-based Atherosclerosis Data

“…We propose to use a methodology based on using and integrating available data sources describing genes, gender, and age associated with gene donors. The methodology uses the following data sources: (i) T2DiACoD database [30]; (ii) GTEx database [34,35], (iii) STRING network database [36]. The methodology also uses voyAGEr [37] to analyse sex differences [17], and GTexVisualiser to access the GTEx database.…”

“…Expression data are measured as Transcript per Million (TPM). This data integration and gene enrichment process was performed using an ad-hoc realised script that has been integrated into GTExVisualizer [17,34]. The integrated data are reported in the data matrix whose snapshot is reported in Figure 1, while the entire data is available at https: //drive.google.com/drive/folders/1-YpCRGdN_UtdS_3hEKrF7_Icbhq_V09d.…”

Non Parametric Differential Network Analysis: A Tool for Unveiling Specific Molecular Signatures

“…Focusing on atherosclerosis, we obtained a list of 115 genes related to this disease in T2DiACoD database, while for diabetes we obtained a list of 650 genes. We retrieved expression data by employing GTExVisualizer [8, 28], and metadata related to tissue, sex and age of the sample are extracted using genes identified in the T2DiACoD database in the previous step. Expression data are measured as Transcript per Million (TPM).…”