Online in silico validation of disease and gene sets, clusterings or subnetworks with DIGEST

Abstract

Abstract As the development of new drugs reaches its physical and financial limits, drug repurposing has become more important than ever. For mechanistically grounded drug repurposing, it is crucial to uncover the disease mechanisms and to detect clusters of mechanistically related diseases. Various methods for computing candidate disease mechanisms and disease clusters exist. However, in the absence of ground truth, in silico validation is challenging. This constitutes a major hurdle toward the adoption of in silico prediction tools by experimentalists who are often hesitant to carry out wet-lab validations for predicted candidate mechanisms without clearly quantified initial plausibility. To address this problem, we present DIGEST (in silico validation of disease and gene sets, clusterings or subnetworks), a Python-based validation tool available as a web interface (https://digest-validation.net), as a stand-alone package or over a REST API. DIGEST greatly facilitates in silico validation of gene and disease sets, clusterings or subnetworks via fully automated pipelines comprising disease and gene ID mapping, enrichment analysis, comparisons of shared genes and variants and background distribution estimation. Moreover, functionality is provided to automatically update the external databases used by the pipelines. DIGEST hence allows the user to assess the statistical significance of candidate mechanisms with regard to functional and genetic coherence and enables the computation of empirical $P$-values with just a few mouse clicks.