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bioRxiv · 10.1101/2024.10.23.619445

Genular: An Integrated Platform for Defining Cellular Identity and Function through Single-Cell Gene Expression and Multi-Domain Biological Data

Tomic, I.·Hao, S. P.·Tomic, A.
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Abstract

Accurately defining cellular identity and function is essential for advancing immunology, understanding disease mechanisms, and developing targeted therapies. However, current bioinformatics tools are limited in their ability to integrate and analyze the vast and diverse single-cell RNA sequencing (scRNA-seq) datasets available, hindering the comprehensive capture of cellular heterogeneity and the identification of subtle genetic changes across immune states, differentiation pathways, and tissue contexts. To overcome these challenges, we introduce genular, an open-source platform that unifies gene expression data analysis across diverse cell types by integrating scRNA-seq data with extensive genomic and proteomic information from 16 databases, including NCBI Gene, Human Protein Atlas, STRING, and UniProt. genular aggregates data from more than 2,893 scRNA-seq experiments, encompassing over 74.5 million unique cells across various tissues and conditions. A key feature of genular is calculating a cell marker score for each gene, enabling the quantification of gene expression across cells to derive unique profiles specific to cell types, states, and lineages. Using genular, we differentiate T cell memory states, map differentiation profiles by tracking gene expression changes as monocytes mature into macrophages and lymphoid progenitor cells develop into T cells, and capture tissue-specific reprogramming of macrophages, revealing distinct gene expression profiles that enable specialized functions in different tissues. By integrating scRNA-seq data with multi-domain biological information and employing advanced statistical methodologies, genular provides a scalable platform that accurately defines cellular identities, functional states, and differentiation pathways. This comprehensive approach facilitates breakthroughs in immunology, gene regulation, cellular differentiation, and disease research, enabling a deeper understanding of immune cell functions and their roles in health and disease.

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Tomic, I., Hao, S. P., Tomic, A.. 2024-10-28. Genular: An Integrated Platform for Defining Cellular Identity and Function through Single-Cell Gene Expression and Multi-Domain Biological Data. https://doi.org/10.1101/2024.10.23.619445

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