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The single-sample network module biomarkers (sNMB) method reveals the pre-deterioration stage of disease progression
Jiayuan Zhong1,2 , Huisheng Liu4 , Pei Chen2,3,*
1School of Mathematics and Big Data, Foshan University, Foshan 528000, China
2School of Mathematics, South China University of Technology, Guangzhou 510640, China
3Pazhou Lab, Guangzhou 510330, China
4School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
*Correspondence to:Pei Chen ,
J Mol Cell Biol, Volume 14, Issue 8, August 2022, mjac052,

The progression of complex diseases generally involves a pre-deterioration stage that occurs during the transition from a healthy state to disease deterioration, at which a drastic and qualitative shift occurs. The development of an effective approach is urgently needed to identify such a pre-deterioration stage or critical state just before disease deterioration, which allows the timely implementation of appropriate measures to prevent a catastrophic transition. However, identifying the pre-deterioration stage is a challenging task in clinical medicine, especially when only a single sample is available for most patients, which is responsible for the failure of most statistical methods. In this study, a novel computational method, called single-sample network module biomarkers (sNMB), is presented to predict the pre-deterioration stage or critical point using only a single sample. Specifically, the proposed single-sample index effectively quantifies the disturbance caused by a single sample against a group of given reference samples. Our method successfully detected the early warning signal of the critical transitions when applied to both a numerical simulation and four real datasets, including acute lung injury, stomach adenocarcinoma, esophageal carcinoma, and rectum adenocarcinoma. In addition, it provides signaling biomarkers for further practical application, which helps to discover prognostic indicators and reveal the underlying molecular mechanisms of disease progression.