Work

Transcriptional perturbation effects remain structured beyond the leading global trend

Year: 2026

Type: preprint

Abstract: Prior work has described a global transcriptional response to gene perturbation, with many perturbations moving cells along a common direction. We find that perturbations contribute differently to this leading global trend and that substantial organization remains beyond it, including transferable perturbation-specific effects across datasets and a common hierarchy of responsive genes across perturbations. These patterns make simple strategies surprisingly competitive even in predicting effects beyond the leading global component.

Source: bioRxiv (Cold Spring Harbor Laboratory)

DOI: 10.64898/2026.10.05.756839

Authors: Qiyuan Liu, Qirui Zhang, Yilong Chen, Jinhong Du, Siming Zhao, Jingshu Wang

Institutions: University of Chicago, Dartmouth College, University of Hong Kong, Dartmouth Cancer Center

Language: English

Topic: Gene Regulatory Network Analysis

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: green

Funders: National Science Foundation, National Institute of General Medical Sciences

Award: CAREER: New Challenges in Statistical Genetics: Mendelian Randomization, Integrated Omics and General Methodology