Multi-omics enrichment analysis using the GeneTrail2 web service

TLDR

Gene set analysis has revolutionized the interpretation of high‑throughput transcriptomic data. We present GeneTrail2, a web service that enables integrated analysis of transcriptomic, miRNA, genomic, and proteomic datasets. GeneTrail2 offers multiple statistical tests, extensive reference sets and biological categories, and supports direct comparison of results, as illustrated by its application to Wilms tumor mechanisms. Using GeneTrail2, we uncovered signaling cascades and potential biomarkers in blastemal Wilms tumors and demonstrated its effectiveness for integrative omics analysis of complex diseases.

Abstract

Gene set analysis has revolutionized the interpretation of high-throughput transcriptomic data. Nowadays, with comprehensive studies that measure multiple -omics from the same sample, powerful tools for the integrative analysis of multi-omics datasets are required.Here, we present GeneTrail2, a web service allowing the integrated analysis of transcriptomic, miRNomic, genomic and proteomic datasets. It offers multiple statistical tests, a large number of predefined reference sets, as well as a comprehensive collection of biological categories and enables direct comparisons between the computed results. We used GeneTrail2 to explore pathogenic mechanisms of Wilms tumors. We not only succeeded in revealing signaling cascades that may contribute to the malignancy of blastemal subtype tumors but also identified potential biomarkers for nephroblastoma with adverse prognosis. The presented use-case demonstrates that GeneTrail2 is well equipped for the integrative analysis of comprehensive -omics data and may help to shed light on complex pathogenic mechanisms in cancer and other diseases.GeneTrail2 can be freely accessed under https://genetrail2.bioinf.uni-sb.de: [e-mail] data are available at Bioinformatics online.