Dataset Information

Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis.

ABSTRACT: Single-cell RNA-sequencing has become a powerful tool to study biologically significant characteristics at explicitly high resolution. However, its application on emerging data is currently limited by its intrinsic techniques. Here, we introduce Tissue-AdaPtive autoEncoder (TAPE), a deep learning method connecting bulk RNA-seq and single-cell RNA-seq to achieve precise deconvolution in a short time. By constructing an interpretable decoder and training under a unique scheme, TAPE can predict cell-type fractions and cell-type-specific gene expression tissue-adaptively. Compared with popular methods on several datasets, TAPE has a better overall performance and comparable accuracy at cell type level. Additionally, it is more robust among different cell types, faster, and sensitive to provide biologically meaningful predictions. Moreover, through the analysis of clinical data, TAPE shows its ability to predict cell-type-specific gene expression profiles with biological significance. We believe that TAPE will enable and accelerate the precise analysis of high-throughput clinical data in a wide range.

SUBMITTER: Chen Y

PROVIDER: S-EPMC9641692 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature

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Publications

Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis.

Chen Yanshuo Y Wang Yixuan Y Chen Yuelong Y Cheng Yuqi Y Wei Yumeng Y Li Yunxiang Y Wang Jiuming J Wei Yingying Y Chan Ting-Fung TF Li Yu Y

Nature communications 20221108 1

Single-cell RNA-sequencing has become a powerful tool to study biologically significant characteristics at explicitly high resolution. However, its application on emerging data is currently limited by its intrinsic techniques. Here, we introduce Tissue-AdaPtive autoEncoder (TAPE), a deep learning method connecting bulk RNA-seq and single-cell RNA-seq to achieve precise deconvolution in a short time. By constructing an interpretable decoder and training under a unique scheme, TAPE can predict cel ...[more]

PMID: 36347853

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Project description:MotivationRecent advances in sequencing technology provide opportunities to study biological processes at a higher resolution. Cell type annotation is an important step in scRNA-seq analysis, which often relies on established marker genes. However, most of the previous methods divide the identification of cell types into two stages, clustering and assignment, whose performances are susceptible to the clustering algorithm, and the marker information cannot effectively guide the clustering process. Furthermore, their linear heuristic-based cell assignment process is often insufficient to capture potential dependencies between cells and types.ResultsHere, we present Interpretable Cell Type Annotation based on self-training (sICTA), a marker-based cell type annotation method that combines the self-training strategy with pseudo-labeling and the nonlinear association capturing capability of Transformer. In addition, we incorporate biological priori knowledge of genes and pathways into the classifier through an attention mechanism to enhance the transparency of the model. A benchmark analysis on 11 publicly available single-cell datasets demonstrates the superiority of sICTA compared to state-of-the-art methods. The robustness of our method is further validated by evaluating the prediction accuracy of the model on different cell types for each single-cell data. Moreover, ablation studies show that self-training and the ability to capture potential dependencies between cells and cell types, both of which are mutually reinforcing, work together to improve model performance. Finally, we apply sICTA to the pancreatic dataset, exemplifying the interpretable attention matrix captured by sICTA.Availability and implementationThe source code of sICTA is available in public at https://github.com/nbnbhwyy/sICTA. The processed datasets can be found at https://drive.google.com/drive/folders/1jbqSxacL_IDIZ4uPjq220C9Kv024m9eL. The final version of the model will be permanently available at https://doi.org/10.5281/zenodo.13474010.

Dataset Information

Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis.

Publications

Deep autoencoder for interpretable tissue-adaptive deconvolution and cell-type-specific gene analysis.

Similar Datasets

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