| 黄泽珩，杜志强.应用自编码器插补提高猪早期胚胎单细胞转录组分析精度[J].广东农业科学,2024,51(1):97-107 |
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应用自编码器插补提高猪早期胚胎单细胞转录组分析精度 |
| Application of Autoencoder Interpolation to Enhance the Accuracy of Single-Cell Transcriptomic Analysis in Early Porcine Embryos |
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| DOI：10.16768/j.issn.1004-874X.2024.01.010 |
| 中文关键词: 猪 早期胚胎 单细胞转录组 深度学习 自编码器 |
| 英文关键词: porcine early embryo single-cell transcriptome in-dept learning autoencoder |
| 基金项目:安徽省农作物和畜禽良种联合攻关方案（皖农种函〔2021〕811 号） |
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| 中文摘要: |
| 【目的】自编码器作为一种深度学习算法，在单细胞转录组数据降维和插补分析上具有独特优势。评估自编码器 AutoClass 应用在猪早期胚胎单细胞转录组数据中的可行性，探究不同胚胎激活方式对关键基因和信号传导通路的影响。【方法】收集 3 种不同激活方式（体内受精、体外授精和孤雌激活）的猪早期胚胎单细胞转录组数据，采用 AutoClass 进行数据质控和插补分析，结合下游分析评估 AutoClass 性能。此外，通过差异表达基因（Differential expression genes, DEG）和功能富集分析，比较 3 种类型胚胎的关键基因和信号通路。【结果】经过数据质控和自编码器数据插补，聚类分析精度提高，不同激活方式的猪早期胚胎聚类清晰。单独质控只筛选出 1 287 个 DEG，而自编码器插补后，DEG 数目增加至 11 523 个。功能富集分析进一步挖掘出 3 种不同类型胚胎间显著差异的关键生物学过程和信号通路，如体内受精胚胎的基础生物学过程和细胞代谢，体外授精胚胎的性腺发育和性别决定，以及孤雌生殖胚胎的免疫防御和分泌途径调节。【结论】采用自编码器提高单细胞转录组数据的分析精度，揭示了 3 种胚胎激活方式影响猪早期胚胎发育的关键基因和信号通路，为深入研究猪早期胚胎发育的分子机制提供了新思路。 |
| 英文摘要: |
| 【Objective】Autoencoder, as one of the deep learning algorithms, offers unique advantages in reducing dimensionality and conducting interpolation analysis on single-cell transcriptome data. The study aims to assess the feasibility of applying the autoencoder AutoClass to early porcine embryo single-cell transcriptome data, and to investigate the impacts of different embryonic activation methods on key genes and signaling pathways.【Method】Single-cell transcriptome data were collected from early porcine embryos with 3 different activation modes (in vivo fertilization, in vitro fertilization, and orphaned females), and AutoClass was used to perform data quality control and interpolation analyses and evaluate AutoClass performance in conjunction with downstream analyses. In addition, an in-depth comparison of key genes and signaling pathways in the three types of embryos was performed by differential expression genes (DEGs) and functional enrichment analysis.【Result】After quality control and autoencoder data interpolation, the accuracy of clustering analysis was enhanced, leading to clear clustering among early embryos with different activation methods. QC alone only screened out 1 287 DEGs, while the number of DEGs increased to 11 523 after autocoder interpolation. Functional enrichment analysis further unearthed key biological processes and signaling pathways that were significantly different among the three different types of embryos, such as basic biological processes and cellular metabolism in porcine in vivo fertilized embryos, gonadal development and sex determination in porcine in vitro fertilized embryos and immune defenses and regulation of secretory pathways in orphaned embryos.【Conclusion】The autoencoder was adopted to improve the analytical accuracy of single-cell transcriptome data, whereby the key genes and signaling pathways affecting early embryonic development in three embryonic activation modes were revealed, which provided new ideas for further in-depth study of the molecular mechanisms underlying early embryonic development in porcine. |
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