title: A high-fidelity cell lineage tracing method for obtaining systematic spatiotemporal gene expression patterns in Caenorhabditis elegans.
abstract: Advances in microscopy and fluorescent reporters have allowed us to detect the onset of gene expression on a cell-by-cell basis in a systemic fashion. This information, however, is often encoded in large repositories of images, and developing ways to extract this spatiotemporal expression data is a difficult problem that often uses complex domain-specific methods for each individual data set. We present a more unified approach that incorporates general previous information into a hierarchical probabilistic model to extract spatiotemporal gene expression from 4D confocal microscopy images of developing Caenorhabditis elegans embryos. This approach reduces the overall error rate of our automated lineage tracing pipeline by 3.8-fold, allowing us to routinely follow the C. elegans lineage to later stages of development, where individual neuronal subspecification becomes apparent. Unlike previous methods that often use custom approaches that are organism specific, our method uses generalized linear models and extensions of standard reversible jump Markov chain Monte Carlo methods that can be readily extended to other organisms for a variety of biological inference problems relating to cell fate specification. This modeling approach is flexible and provides tractable avenues for incorporating additional previous information into the model for similar difficult high-fidelity/low error tolerance image analysis problems for systematically applied genomic experiments.
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98103, USA. dlm19@uw.edu
authors.forename: Daniel L
authors.initials: DL
authors.lastname: Mace
authors.forename: Peter
authors.initials: P
authors.lastname: Weisdepp
authors.forename: Louis
authors.initials: L
authors.lastname: Gevirtzman
authors.forename: Thomas
authors.initials: T
authors.lastname: Boyle
authors.forename: Robert H
authors.initials: RH
authors.lastname: Waterston
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000166:cytology* / Q000235:genetics*; D029742:Caenorhabditis elegans Proteins / Q000378:metabolism; D002454:Cell Differentiation / Q000235:genetics; D019070:Cell Lineage / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D008040:Genetic Linkage; D018398:Homeodomain Proteins / Q000378:metabolism; D008954:Models, Biological; D009479:Neuropeptides / Q000378:metabolism; D015203:Reproducibility of Results; D062211:Spatio-Temporal Analysis
chemical_list: D029742:Caenorhabditis elegans Proteins; D018398:Homeodomain Proteins; D009479:Neuropeptides; C108368:TTX-3 protein, C elegans
keywords: C. elegans; cell fate; gene expression; image analysis; lineage
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