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

dc.contributor.authorZhang, Pengyue
dc.contributor.authorMourad, Raphaël
dc.contributor.authorXiang, Yang
dc.contributor.authorHuang, Kun
dc.contributor.authorHuang, Tim
dc.contributor.authorNephew, Kenneth
dc.contributor.authorLiu, Yunlong
dc.contributor.authorLi, Lang
dc.contributor.departmentCenter for Computational Biology and Bioinformatics, School of Medicine
dc.date.accessioned2025-05-30T07:45:48Z
dc.date.available2025-05-30T07:45:48Z
dc.date.issued2012
dc.description.abstractBackground: 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. Results: 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). Conclusions: 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.
dc.eprint.versionFinal published version
dc.identifier.citationZhang P, Mourad R, Xiang Y, et al. A dynamic time order network for time-series gene expression data analysis. BMC Syst Biol. 2012;6 Suppl 3(Suppl 3):S9. doi:10.1186/1752-0509-6-S3-S9
dc.identifier.urihttps://hdl.handle.net/1805/48472
dc.language.isoen_US
dc.publisherSpringer Nature
dc.relation.isversionof10.1186/1752-0509-6-S3-S9
dc.relation.journalBMC Systems Biology
dc.rightsAttribution 4.0 Internationalen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.sourcePMC
dc.subjectEstradiol
dc.subjectBreast neoplasms
dc.subjectCluster analysis
dc.subjectGenetic markers
dc.titleA dynamic time order network for time-series gene expression data analysis
dc.typeArticle
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