ECGA: A web server to explore and analyze extrachromosomal gene in cancer.

Circular extrachromosomal DNA (ecDNA) plays a crucial role in the onset, progression, and evolution of many types of cancers, with dysregulated gene expression driven by ecDNA as a key mechanism. Although database resources for ecDNA are now available, a sophisticated web application dedicated to ecDNA gene analysis remains absent. Therefore, we developed ecDNA gene analyzer (ECGA). ECGA catalogues 23,274 unique ecDNA genes of 27 cancers across 27 tissues. ECGA also offers five specialized analysis tools: (1) 'Venn analysis' looks for overlaps between a given gene list and ecDNA genes; (2) 'Enrichment analysis' performs over-representation analysis and gene set enrichment analysis of input gene list within predefined ecDNA gene sets; (3) 'Target discovery' identifies upregulated ecDNA genes as targets by comparing with reference expression in normal samples; (4) 'DE analysis' finds differentially expressed ecDNA genes; (5) 'Signature discovery' discerns ecDNA gene signatures capable of classifying samples into phenotypic groups, and it is accompanied by 'Signature validation' for model test on unseen data. In summary, ECGA emerges as an indispensable platform in cancer genetics, bridging gaps in basic research, medical reporting, and pharmaceutical development, and propelling ecDNA research forward. ECGA is freely available at https://www.zhounan.org/ecga/.