Bayesian detection of embryonic gene expression onset in \textit{C. elegans}

DOI10.1214/15-AOAS820zbMATH Open1454.62345arXiv1509.04872OpenAlexW3098322941MaRDI QIDQ746687FDOQ746687

Authors: Jie Hu, Zhongying Zhao, Hari Krishna Yalamanchili, Junwen Wang, Xiaodan Fan, Kenny Q. Ye 

Publication date: 28 October 2015

Published in: The Annals of Applied Statistics (Search for Journal in Brave)

Abstract: To study how a zygote develops into an embryo with different tissues, large-scale 4D confocal movies of C. elegans embryos have been produced recently by experimental biologists. However, the lack of principled statistical methods for the highly noisy data has hindered the comprehensive analysis of these data sets. We introduced a probabilistic change point model on the cell lineage tree to estimate the embryonic gene expression onset time. A Bayesian approach is used to fit the 4D confocal movies data to the model. Subsequent classification methods are used to decide a model selection threshold and further refine the expression onset time from the branch level to the specific cell time level. Extensive simulations have shown the high accuracy of our method. Its application on real data yields both previously known results and new findings.

Full work available at URL: https://arxiv.org/abs/1509.04872

Recommendations

• Statistical stage transition detection method for small sample gene expression time series data
• Functional Hierarchical Models for Identifying Genes with Different Time‐Course Expression Profiles
• A Bayesian Mixture Model for Partitioning Gene Expression Data
• A Bayesian Approach to Estimation and Testing in Time-course Microarray Experiments
• An empirical Bayes change-point model for transcriptome time-course data

zbMATH Keywords

change point detectionBayesian method4D confocal microscopyembryonic onset

Mathematics Subject Classification ID

Computational methods for problems pertaining to statistics (62-08) Applications of statistics to biology and medical sciences; meta analysis (62P10)

Cites Work

• Inference from iterative simulation using multiple sequences
• Testing and estimating change-points in time series
• Bayesian detection of embryonic gene expression onset in \textit{C. elegans}

Cited In (4)

• Correlation for tree-shaped datasets and its Bayesian estimation
• Bayesian detection of event spreading pattern from multivariate binary time series
• Bayesian detection of embryonic gene expression onset in \textit{C. elegans}
• A Bayesian statistical analysis of stochastic phenotypic plasticity model of cancer cells

This page was built for publication: Bayesian detection of embryonic gene expression onset in \textit{C. elegans}

Report a bug (only for logged in users!)Click here to report a bug for this page (MaRDI item Q746687)