AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution
Aliee H, Theis F (2021)
Publication Type: Journal article
Publication year: 2021
Journal
Book Volume: 12
Pages Range: 706-715.e4
Journal Issue: 7
DOI: 10.1016/j.cels.2021.05.006
Abstract
Knowing cell-type proportions in a tissue is very important to identify which cells or cell types are targeted by a disease or perturbation. Hence, several deconvolution methods have been proposed to infer cell-type proportions from bulk RNA samples. Their performance with noisy reference profiles and closely correlated cell types highly depends on the set of genes undergoing deconvolution. In this work, we introduce AutoGeneS, a platform that automatically extracts discriminative genes and reveals the cellular heterogeneity of bulk RNA samples. AutoGeneS requires no prior knowledge about marker genes and selects genes by simultaneously optimizing multiple criteria: minimizing the correlation and maximizing the distance between cell types. AutoGeneS can be applied to reference profiles from various sources like single-cell experiments or sorted cell populations. Ground truth cell proportions analyzed by flow cytometry confirmed the accuracy of AutoGeneS in identifying cell-type proportions. AutoGeneS is available for use via a standalone Python package (https://github.com/theislab/AutoGeneS).
Involved external institutions
Germany (DE)How to cite
APA:
Aliee, H., & Theis, F. (2021). AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution. Cell Systems, 12(7), 706-715.e4. https://dx.doi.org/10.1016/j.cels.2021.05.006
MLA:
Aliee, Hananeh, and Fabian Theis. "AutoGeneS: Automatic gene selection using multi-objective optimization for RNA-seq deconvolution." Cell Systems 12.7 (2021): 706-715.e4.
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