A dynamic time order network for time-series gene expression data analysis

BMC Systems Biology
Pengyue ZhangLang Li

Abstract

Typical analysis of time-series gene expression data such as clustering or graphical models cannot distinguish between early and later drug responsive gene targets in cancer cells. However, these genes would represent good candidate biomarkers. We propose a new model - the dynamic time order network - to distinguish and connect early and later drug responsive gene targets. This network is constructed based on an integrated differential equation. Spline regression is applied for an accurate modeling of the time variation of gene expressions. Then a likelihood ratio test is implemented to infer the time order of any gene expression pair. One application of the model is the discovery of estrogen response biomarkers. For this purpose, we focused on genes whose responses are late when the breast cancer cells are treated with estradiol (E2). Our approach has been validated by successfully finding time order relations between genes of the cell cycle system. More notably, we found late response genes potentially interesting as biomarkers of E2 treatment.

References

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Citations

Jan 11, 2013·BMC Systems Biology·Yufei HuangBing Zhang
Dec 3, 2014·Developmental Biology·Thomas HaDan Goldowitz
May 10, 2019·International Journal of Molecular Sciences·Hassan DastsoozSalvatore Oliviero

Related Concepts

Mammary Neoplasms, Human
Cell Cycle
Estradiol, (16 alpha,17 beta)-Isomer
Genetic Markers
Poly(A) Tail
Gene Expression Regulation, Neoplastic
Disease Clustering
Computational Molecular Biology
MRNA Differential Display
Online Mendelian Inheritance In Man

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