MLHeatmap: an interactive application for transcriptomic marker-panel discovery

Abstract

Abstract Motivation Transcriptomic biomarker studies often require separate tools for normalization, classification, feature ranking, and visualization. MLHeatmap was developed to integrate these steps into a cross-platform, browser-based workflow and to support compact marker-panel discovery directly from count matrices. Results MLHeatmap accepts a count matrix and sample-group labels and performs gene mapping, normalization, multiclass classification with nested cross-validation, feature attribution, differential expression analysis, and interactive heatmap visualization, with support for multiple classifiers and panel-selection methods in the same workflow. As a case study, we applied MLHeatmap to colorectal cancer consensus molecular subtype (CMS) classification using 511 primary tumors from The Cancer Genome Atlas (TCGA) with published Colorectal Cancer Subtyping Consortium (CRCSC) labels. Random Forest with forward selection achieved 89.8% out-of-fold accuracy and a macro-averaged area under the receiver operating characteristic curve (macro AUC) of 0.973, yielding a 13-gene compact panel with a held-out AUC of 0.960. External validation of the compact panel gave 74.8% accuracy and a macro AUC of 0.917 in GSE39582, an independent Affymetrix GPL570 microarray cohort evaluated in 500 tumors with confident CMScaller-derived CMS assignments, and 69.18% accuracy and a macro AUC of 0.909 in CMCBSN, an independent Korean RNA-seq cohort with 159 confidently labeled tumors. Across the five classifiers and four panel-selection methods evaluated, compact-panel AUCs ranged from 0.895 to 0.970, with tree-ensemble classifiers reaching the highest values. Availability and implementation MLHeatmap is freely available at https://github.com/kangk1204/MLHeatmap and can be installed and run locally on Windows 11, macOS, and Ubuntu.