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Fig. 1 | Genome Medicine

Fig. 1

From: Large-scale public data reuse to model immunotherapy response and resistance

Fig. 1

TIDE web platform architecture. The TIDE web platform aims to facilitate the hypothesis generation, biomarker optimization, and patient stratification in immune-oncology research through a public data reuse approach. The platform functions are based on the integration of large-scale omics data and biomarkers on published ICB trials, non-immunotherapy tumor profiles, and CRISPR screens. The web platform takes gene set or expression profiles as input and provides three interactive modules. A Gene prioritization for a user-input gene set. Every gene is ranked by their clinical relevance and CRISPR screen phenotype, including four types of metrics: 1, the association between gene expression and T cell dysfunction across cohorts, computed as the z-score in the Cox Proportional Hazard (PH) regression model; 2, the association between gene expression and ICB response across tumors, computed as the z-score in the Cox-PH regression; 3, the log-fold change in CRISPR screens probing the effect of gene knockout on lymphocyte-mediated tumor killing; 4, the gene expression in cell types driving T cell exclusion in tumors. Data cohorts are grouped by their metric types on the heatmap (columns). Genes (rows) can be interactively reordered by the gene values either on a single data set or any metric type groups. B Biomarker evaluation for a custom biomarker gene set. The predictive power of biomarkers in the public immunotherapy cohorts is quantified by two criteria, the area under the receiver operating characteristic curve (AUC) and the z-score in the Cox-PH regression. We visualize biomarkers’ AUC by bar plots (left panel) and Cox-PH z-scores by Kaplan-Meier curve (right panel). C Biomarker consensus to predict ICB response from gene expression profile. Every input transcriptomic profile is evaluated by TIDE, microsatellite instability (MSI) signature, interferon-gamma (IFNG) signature, and other biomarkers reported in the literature

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