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Real age prediction from the transcriptome with RAPToR

View ORCID ProfileRomain Bulteau, View ORCID ProfileMirko Francesconi
doi: https://doi.org/10.1101/2021.09.07.459270
Romain Bulteau
1Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR5239, U 1210, F-69364 Lyon, France
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Mirko Francesconi
1Laboratoire de Biologie et Modélisation de la Cellule, Université de Lyon, ENS, UCBL, CNRS, INSERM, UMR5239, U 1210, F-69364 Lyon, France
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  • For correspondence: mirko.francesconi@ens-lyon.fr
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Abstract

Genome-wide gene expression profiling is a powerful tool for exploratory analyses, providing a high dimensional picture of the state of a biological system. However, uncontrolled variation among samples can obscure and confound the effect of variables of interest. Uncontrolled developmental variation is often a major source of unknown expression variation in developmental systems. Existing methods to sort samples from transcriptomes require many samples to infer developmental trajectories and only provide a relative pseudo-time.

Here we present RAPToR (Real Age Prediction from Transcriptome staging on Reference), a simple computational method to estimate the absolute developmental age of even a single sample from its gene expression with up to minutes precision. We achieve this by staging samples on high-resolution reference developmental expression profiles we build from existing time series data. We implemented RAPToR for the most common animal model systems: nematode, fruit fly, zebrafish, and mouse, and demonstrate application for non-model organisms. We show how developmental variation discovered by RAPToR can be exploited to increase power to detect differential expression and to untangle the signal of perturbations of interest even when it is completely confounded with development. We anticipate our RAPToR post-profiling staging strategy will be especially useful in large scale single organism profiling because it eliminates the need for synchronization or for a tedious and potentially difficult step of accurate staging before profiling.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted September 08, 2021.
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Real age prediction from the transcriptome with RAPToR
Romain Bulteau, Mirko Francesconi
bioRxiv 2021.09.07.459270; doi: https://doi.org/10.1101/2021.09.07.459270
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Real age prediction from the transcriptome with RAPToR
Romain Bulteau, Mirko Francesconi
bioRxiv 2021.09.07.459270; doi: https://doi.org/10.1101/2021.09.07.459270

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