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

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, many analytical functions researchers require remain adequately unmet by these tools. Thus, we introduce BEST (Biomarker Exploration for Solid Tumors), a web application for comprehensive biomarker exploration on large-scale data in solid tumors. BEST includes more than 50,000 samples of 27 cancer types. To ensure the comparability of genes between different sequencing technologies and the legibility of clinical traits, we re-annotated transcriptome data based on the GRCh38 patch 13 sequences 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/.

SurvivalML: an integrative platform for the discovery and exploration of prognostic models in multi-center cancer cohorts

“…Our team developed a web server (BEST, https://rookieutopia.com/app_direct/BEST/) for comprehensive biomarker exploration on multi-center transcriptome data in solid tumors 29 . BEST enabled users to explore a single gene or gene list in according to the following eight aspects: clinical association, survival analysis, enrichment analysis, cell infiltration, immunomodulator, immunotherapy, candidate agents, and genomic alteration (Figure 1).…”

“…In addition, we provided an extra interface to the BEST web server, which was also developed by our team 29 . BEST enables users to explore the clinical significance and biological peculiarities of a single gene or gene list.…”

Deciphering cutaneous melanoma prognosis through LDL metabolism: Single‐cell transcriptomics analysis via 101 machine learning algorithms

“…To assess the prognostic value, the overall survival rate (OS) and disease‐specific survival rate (DSS) of the key gene in the TCGA cohort were evaluated using the BEST database 25 . Additionally, univariate COX regression analysis was conducted, in conjunction with the dataset containing survival status information for skin melanoma from the GEO database.…”

Distinct roles of CD244 expression in cancer diagnosis and prognosis: A pan-cancer analysis

“…Furthermore, eight tissue samples of UCEC from DISCO database [ 26 ] were used to analyze the relationship between CD244 and immune infiltrating at single cell level. Moreover, we used BEST database [ 27 ] to explore the relationship between CD244 expression and immunotherapy response in cancer patients.…”