COMPASS: A Web-Based COMPosite Activity Scoring System to Navigate Health and Disease Through Deterministic Digital Biomarkers
Abstract
Quantifying pathway activation in absolute, reproducible terms is central to systems biology and precision medicine. COMPASS (COMPosite Activity Scoring System; https://compass.precsn.com/) provides a deterministic, ontology-free framework that defines gene-specific thresholds and aggregates standardized deviations into composite digital biomarkers of pathway activation. By transforming raw expression data into interpretable, data-anchored metrics, COMPASS delivers a transparent, reproducible, and scalable means to integrate, align, and benchmark ‘humanness’ across digital and experimental model systems, bringing computational rigor, regulatory reproducibility, and experimental relevance at the fingertips of every biologist.
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Supplemental Figure and legend Figure S1. Computational Workflow and User Interface of COMPASS.
(a) Workflow schematic. From a user-supplied expression matrix (txt/tsv/csv) and a selected gene signature with optional weights and sample groups, COMPASS applies StepMiner thresholding, computes standardized deviations, aggregates weighted deviations, and benchmarks pathway activity with ROC–AUC against biological or clinical states. Outputs include downloadable box plots (multi-group comparisons with multiple statistical tests) and ROC/AUC reports with F statistics. (b) User interface. Steps and associated screenshots illustrate the web app’s tabs: Data Upload, Gene Signature & Groups, Box Plot & Statistics, and ROC–AUC & Statistics, highlighting a code-free workflow with automatic backend computation, mathematical transparency, and publication-ready downloads. The example demonstrates group stratification (PAM50 breast cancer subtypes using a Breast Cancer index composite score) and with statistical significance.