PreDigs: A Database of Context-specific Cell-type Markers and Precise Cell Subtypes for Digestive Cell Annotation.

Abstract

Research on cell type markers helps investigators explore the diverse cellular compositions of gastrointestinal tumors. This enhances our understanding of tumor heterogeneity and its impact on disease progression and treatment response. However, integrating large-scale datasets and the lack of standardized cell type identification remain challenges. Here, we developed PreDigs, a user-friendly database of predicted signatures in digestive system, which offers 124 curated single-cell RNA sequencing datasets, covering over 3.4 million cells, all available for download. After unsupervised clustering, we unified the identification and naming of subtype labels, constructing a cell ontology tree with 142 cell types across eight hierarchical levels. Meanwhile, we calculated three different context-specific cell-type markers, including "Cell Markers", "Subtype Markers", and "TPN Markers", based on various application requirements within or across tissues. Through the integrated analysis of PreDigs data, we identified distinct cell subpopulations exclusive to tumors, one of which corresponds to tumor-specific endothelial cells. Additionally, PreDigs offers online cell annotation tools, allowing users to classify single cells with greater flexibility. PreDigs is accessible at https://www.biosino.org/predigs/.