Single-sample landscape entropy reveals the imminent phase transition during disease progression

• Published in: Bioinformatics Vol. 36; no. 5; pp. 1522 - 1532
• Main Authors: Liu, Rui, Chen, Pei, Chen, Luonan
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 01.03.2020
• DOI: 10.1093/bioinformatics/btz758
• ISSN: 1367-4803; 1367-4811

Abstract Motivation The time evolution or dynamic change of many biological systems during disease progression is not always smooth but occasionally abrupt, that is, there is a tipping point during such a process at which the system state shifts from the normal state to a disease state. It is challenging to predict such disease state with the measured omics data, in particular when only a single sample is available. Results In this study, we developed a novel approach, i.e. single-sample landscape entropy (SLE) method, to identify the tipping point during disease progression with only one sample data. Specifically, by evaluating the disorder of a network projected from a single-sample data, SLE effectively characterizes the criticality of this single sample network in terms of network entropy, thereby capturing not only the signals of the impending transition but also its leading network, i.e. dynamic network biomarkers. Using this method, we can characterize sample-specific state during disease progression and thus achieve the disease prediction of each individual by only one sample. Our method was validated by successfully identifying the tipping points just before the serious disease symptoms from four real datasets of individuals or subjects, including influenza virus infection, lung cancer metastasis, prostate cancer and acute lung injury. Availability and implementation https://github.com/rabbitpei/SLE. Supplementary information Supplementary data are available at Bioinformatics online.