Department of Physics, Chuo University, Tokyo, Japan.
Division of Biomedical Information Analysis, Iwate Tohoku Medical Megabank Organization, Disaster Reconstruction Center, Iwate Medical University, Iwate, Japan.
PLoS One. 2023 Aug 9;18(8):e0289029. doi: 10.1371/journal.pone.0289029. eCollection 2023.
Integrating gene expression, DNA methylation, and genomic variants simultaneously without location coincidence (i.e., irrespective of distance from each other) or pairwise coincidence (i.e., direct identification of triplets of gene expression, DNA methylation, and genomic variants, and not integration of pairwise coincidences) is difficult. In this study, we integrated gene expression, DNA methylation, and genome variants from the iMETHYL database using the recently proposed kernel tensor decomposition-based unsupervised feature extraction method with limited computational resources (i.e., short CPU time and small memory requirements). Our methods do not require prior knowledge of the subjects because they are fully unsupervised in that unsupervised tensor decomposition is used. The selected genes and genomic variants were significantly targeted by transcription factors that were biologically enriched in KEGG pathway terms as well as in the intra-related regulatory network. The proposed method is promising for integrated analyses of gene expression, methylation, and genomic variants with limited computational resources.
同时整合基因表达、DNA 甲基化和基因组变异，而不考虑位置巧合（即彼此之间没有距离）或两两巧合（即直接识别基因表达、DNA 甲基化和基因组变异的三联体，而不是整合两两巧合）是困难的。在这项研究中，我们使用最近提出的基于核张量分解的无监督特征提取方法，在有限的计算资源（即短 CPU 时间和小内存需求）下整合了 iMETHYL 数据库中的基因表达、DNA 甲基化和基因组变异。由于使用了无监督张量分解，我们的方法不需要事先了解对象，因为它们是完全无监督的。选择的基因和基因组变异显著靶向转录因子，这些转录因子在 KEGG 通路术语以及内在相关的调控网络中具有生物学富集性。该方法有望在有限的计算资源下进行基因表达、甲基化和基因组变异的综合分析。
