BEST: a web application for comprehensive biomarker exploration on large-scale data in solid tumors

TLDR

Data mining of RNA‑seq or microarray data is essential for cancer biomarker discovery, yet current web servers are limited to single TCGA cohorts and lack meta‑analysis across multiple datasets, leaving biomarker performance thin and unstable and omitting deeper mechanistic, microenvironment, and drug‑indication insights. We introduce BEST, a web application for comprehensive biomarker exploration on large‑scale solid‑tumor data. BEST re‑annotates transcriptome data and standardizes clinical trait nomenclature, then offers fast, customizable analyses including clinical association, survival, enrichment, cell infiltration, immunomodulators, immunotherapy, candidate agents, and genomic alteration. The server provides multiple cleaned independent datasets and diverse analytical functions, enabling users to unlock the value of existing data resources; it is freely available at https://rookieutopia.com/.

Abstract

Abstract Data mining from RNA-seq or microarray data has become an essential part of cancer biomarker exploration. Certain existing web servers are valuable and broadly utilized, but the meta-analysis of multiple datasets is absent. Most web servers only contain tumor samples from the TCGA database with only one cohort for each cancer type, which also means that the analysis results mainly derived from a single cohort are thin and unstable. Indeed, consistent performance across multiple independent cohorts is the foundation for an excellent biomarker. Moreover, the deeper exploration of specific biomarkers on underlying mechanisms, tumor microenvironment, and drug indications are missing in existing tools. Thus, we introduce BEST (Biomarker Exploration for Solid Tumors), a web application for comprehensive biomarker exploration on large-scale data in solid tumors. To ensure the comparability of genes between different sequencing technologies and the legibility of clinical traits, we re-annotated transcriptome data and unified the nomenclature of clinical traits. BEST delivers fast and customizable functions, including clinical association, survival analysis, enrichment analysis, cell infiltration, immunomodulator, immunotherapy, candidate agents, and genomic alteration. Together, our web server provides multiple cleaned-up independent datasets and diverse analysis functionalities, helping unleash the value of current data resources. It is freely available at https://rookieutopia.com/ .