联合建模剪接与未剪接 RNA 可提升单细胞表达数据的信息量
Joint representation of spliced and unspliced RNA expands information content in single-cell expression data
研究提出将单细胞 RNA-seq 中的成熟（剪接）与新生（未剪接）转录本计数作为两类独立特征，而非合并为单一表达矩阵，以检验这种处理能否增加无监督降维可恢复的潜在结构。作者在四个数据集上对仅剪接、仅未剪接、相加和拼接四种表示分别做非负矩阵分解，并通过交叉验证估计可揭示秩，即能达到接近最优留出误差的最大稳定秩。拼接表示在四个数据集上均优于相加表示，并在其中三个上超过任一单模态输入，说明保留剪接状态能暴露超出单模态及其加和的稳定潜在程序。剪接与未剪接来源的因子重叠很少，对应的基因集富集分别指向稳态与新生调控活动。
来源：Bioinformatics Advances · doi.org
Motivation
Single-cell RNA-seq captures both mature (spliced) and nascent (unspliced) transcripts, yet standard preprocessing collapses these signals into a single expression matrix, obscuring recoverable structure and introducing splicing-dependent artifacts in downstream analysis. We asked whether treating spliced and unspliced counts as distinct feature sets increases recoverable latent structure in unsupervised dimension reduction.
Results
Across four datasets, we applied non-negative matrix factorization to spliced-only, unspliced-only, added, and concatenated representations, estimating the revealable rank, the largest stable rank achieving near-optimal held-out error, by cross-validation. Concatenated representations exceeded the added representation in all four datasets and surpassed both single-modality inputs in three of four, indicating that preserving splicing status exposes additional stable latent programs beyond either modality alone or their sum. Minimal overlap between spliced- and unspliced-derived factors corresponded to modality-specific gene set enrichment consistent with complementary steady-state and nascent regulatory activity. These results establish splicing status as an informative axis of variation and motivate preserving spliced and unspliced layers as first-class features to maximize information recovery.
Availability and Implementation
The singlet R package is available at github.com/zdebruine/singlet. Code to reproduce all figures is available at github.com/Arya-86/nmf-spliced-unspliced.
Supplementary information
Supplementary data are appended to this manuscript.