GEPIA2: an enhanced web server for large-scale expression profiling and interactive analysis

TLDR

GEPIA, launched in 2017, has been a widely cited resource for gene expression analysis using TCGA and GTEx tumor and normal samples. GEPIA2 is introduced as an updated, enhanced version offering higher resolution and additional functionalities. GEPIA2 expands analysis to 198,619 isoforms across 84 cancer subtypes, supports subtype comparison, incorporates single‑cell inspired gene‑signature quantification, allows user‑uploaded RNA‑seq data, and provides an API for batch retrieval. The updated server is publicly available at http://gepia2.cancer-pku.cn.

Abstract

Abstract Introduced in 2017, the GEPIA (Gene Expression Profiling Interactive Analysis) web server has been a valuable and highly cited resource for gene expression analysis based on tumor and normal samples from the TCGA and the GTEx databases. Here, we present GEPIA2, an updated and enhanced version to provide insights with higher resolution and more functionalities. Featuring 198 619 isoforms and 84 cancer subtypes, GEPIA2 has extended gene expression quantification from the gene level to the transcript level, and supports analysis of a specific cancer subtype, and comparison between subtypes. In addition, GEPIA2 has adopted new analysis techniques of gene signature quantification inspired by single-cell sequencing studies, and provides customized analysis where users can upload their own RNA-seq data and compare them with TCGA and GTEx samples. We also offer an API for batch process and easy retrieval of the analysis results. The updated web server is publicly accessible at http://gepia2.cancer-pku.cn/.