# Systematic evaluation of the isolated effect of tissue environment on the transcriptome using a single-cell RNA-seq atlas dataset

## TL;DR

This study introduces a new method to analyze how tissue environments affect gene expression in single cells, revealing important insights into immune responses and aging.

## Contribution

The study introduces COSER, a novel framework using graph theory to reduce confounding and assess isolated tissue environment effects on gene expression.

## Key findings

- Some genes are significantly influenced by tissue environments, especially in immune responses.
- COSER reveals age-related changes in intercellular diversity linked to tissue environments.
- COSER is a robust and general-purpose tool for analyzing large-scale single-cell data.

## Abstract

Understanding cellular diversity throughout the body is essential for elucidating the complex functions of biological systems. Recently, large-scale single-cell omics datasets, known as omics atlases, have become available. These atlases encompass data from diverse tissues and cell-types, providing insights into the landscape of cell-type-specific gene expression. However, the isolated effect of the tissue environment has not been thoroughly investigated. Evaluating this isolated effect is challenging due to statistical confounding with cell-type effects, which arises from the highly limited subset of tissue-cell-type combinations that are biologically realized compared to the vast number of theoretical possibilities.

This study introduces a novel data analysis framework, named the Combinatorial Sub-dataset Extraction for Confounding Reduction (COSER), which addresses statistical confounding by using graph theory to enumerate appropriate sub-datasets. COSER enables the assessment of isolated effects of discrete variables in single cells. Applying COSER to the Tabula Muris Senis single-cell transcriptome atlas, we characterized the isolated impact of tissue environments. Our findings demonstrate that some genes are markedly affected by the tissue environment, particularly in modulating intercellular diversity in immune responses and their age-related changes.

COSER provides a robust, general-purpose framework for evaluating the isolated effects of discrete variables from large-scale data mining. This approach reveals critical insights into the interplay between tissue environments and gene expression.

The online version contains supplementary material available at 10.1186/s12864-025-11614-w.