Time series experimental design under one-shot sampling: The importance of condition diversity

Xiaohan Kang, Bruce Hajek, Faqiang Wu, Yoshie Hanzawa

Research output: Contribution to journalArticle

Abstract

Many biological data sets are prepared using one-shot sampling, in which each individual organism is sampled at most once. Time series therefore do not follow trajectories of individuals over time. However, samples collected at different times from individuals grown under the same conditions share the same perturbations of the biological processes, and hence behave as surrogates for multiple samples from a single individual at different times. This implies the importance of growing individuals under multiple conditions if one-shot sampling is used. This paper models the condition effect explicitly by using condition-dependent nominal mRNA production amounts for each gene, it quantifies the performance of network structure estimators both analytically and numerically, and it illustrates the difficulty in network reconstruction under one-shot sampling when the condition effect is absent. A case study of an Arabidopsis circadian clock network model is also included.

Original languageEnglish (US)
Article numbere0224577
JournalPloS one
Volume14
Issue number10
DOIs
StatePublished - Oct 2019

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

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