A joint analysis of single cell transcriptomics and proteomics using transformer
Abstract CITE-seq provides a powerful method for simultaneously measuring RNA and protein expression at the single-cell level. The integrated analysis of RNA and protein expression in identical cells is crucial for revealing cellular heterogeneity. However, the high experimental costs associated wit...
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| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-01-01
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| Series: | npj Systems Biology and Applications |
| Online Access: | https://doi.org/10.1038/s41540-024-00484-9 |
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| Summary: | Abstract CITE-seq provides a powerful method for simultaneously measuring RNA and protein expression at the single-cell level. The integrated analysis of RNA and protein expression in identical cells is crucial for revealing cellular heterogeneity. However, the high experimental costs associated with CITE-seq limit its widespread application. In this paper, we propose scTEL, a deep learning framework based on Transformer encoder layers, to establish a mapping from sequenced RNA expression to unobserved protein expression in the same cells. This computation-based approach significantly reduces the experimental costs of protein expression sequencing. We are now able to predict protein expression using single-cell RNA sequencing (scRNA-seq) data, which is well-established and available at a lower cost. Moreover, our scTEL model offers a unified framework for integrating multiple CITE-seq datasets, addressing the challenge posed by the partial overlap of protein panels across different datasets. Empirical validation on public CITE-seq datasets demonstrates scTEL significantly outperforms existing methods. |
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| ISSN: | 2056-7189 |