LiverHomo: An Integrated and Interactive Human Liver Single-Cell Atlas with Protein Interaction and Cell–Cell Communication Networks

Abstract

LiverHomo is an integrated single-cell atlas comprising 1,157,134 cells from 16 publicly available human single-cell RNA-sequencing (scRNA-seq) datasets, spanning healthy and fetal liver tissues, seven major liver diseases, and two tumor-associated contexts: metastatic lymph nodes and portal vein tumor thrombus. Building on existing liver single-cell resources, LiverHomo extends transcriptomic exploration by incorporating predicted protein–protein interaction (PPI) and cell–cell communication (CCI) networks. The resource provides an interactive web portal (https://www.liverhomo.org) for exploring cell-type distributions, gene expression patterns, differential expression, Gene Ontology annotations, and context-specific molecular and intercellular interaction networks across diseases and cell types. To make these multidimensional data easy and intuitive to access, the portal incorporates Ask LiverHomo, an AI-powered virtual assistant that interprets natural-language queries, including multilingual input, and retrieves atlas-derived results and visualizations through predefined analytical functions. Interactive expression plots, network visualizations, and cell-level metadata exploration let users investigate liver biology across cellular, transcriptomic, and molecular interaction levels. The underlying datasets and analytical outputs are available for download to support independent analysis and reuse. Together, LiverHomo provides an integrated and accessible resource for investigating cellular and molecular alterations across human liver health and disease.