A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies
A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies
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DOI：
10.1073/pnas.0709146104
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发表时间：
2007-11-20
影响因子：
11.1
通讯作者：
Alter, Orly
中科院分区：
文献类型：
--
作者：
Omberg, Larsson;Golub, Gene H.;Alter, Orly
我们描述了使用高阶奇异值分解（HOSVD）在转换的数据张量的基因x“x-设置“，也就是说，不同的设置的实验变量x“Y-设置”，它列出了DNA微阵列数据从不同的研究，“核心张量”的“eigenarrays”x“x-eigengenes”x“y-eigengenes。“重新制定这个多线性HOSVD，使其将数据张量分解为一个本征数组的所有外积的线性叠加，一个x-和一个y-本征因子，即秩为1的“子张量”，我们根据它捕获的数据张量中的整体信息的分数来定义每个子张量的重要性。我们说明这HOSVD与整合的基因组规模的mRNA表达数据从三个酵母细胞周期的时间过程中，其中两个下暴露于过氧化氢或甲萘醌。我们发现，显着subtensors代表独立的生物程序或实验现象。出现的图片表明，保守的基因YKU 70，MRE 11，AIF 1和ZWF 1，逆转录转座，细胞凋亡和氧化戊糖磷酸途径，这些基因参与的过程中，可能发挥显着的，但以前未被认识到，在过氧化氢和甲萘醌对细胞周期进程的差异影响的作用。DNA复制起始和RNA转录之间的基因组规模的相关性，这是相当于最近发现的相关性，可能是由于以前未知的调节机制，独立发现。
We describe the use of a higher-order singular value decomposition (HOSVD) in transforming a data tensor of genes x "x-settings,"that is, different settings of the experimental variable x x "Y-settings," which tabulates DNA microarray data from different studies, to a "core tensor" of "eigenarrays" x "x-eigengenes" x "y-eigengenes." Reformulating this multilinear HOSVD such that it decomposes the data tensor into a linear superposition of all outer products of an eigenarray, an x- and a y-eigengene, that is, rank-1 "subtensors," we define the significance of each subtensor in terms of the fraction of the overall information in the data tensor that it captures. We illustrate this HOSVD with an integration of genome-scale mRNA expression data from three yeast cell cycle time courses, two of which are under exposure to either hydrogen peroxide or menadione. We find that significant subtensors represent independent biological programs or experimental phenomena. The picture that emerges suggests that the conserved genes YKU70, MRE11, AIF1, and ZWF1, and the processes of retrotransposition, apoptosis, and the oxidative pentose phosphate pathway that these genes are involved in, may play significant, yet previously unrecognized, roles in the differential effects of hydrogen peroxide and menadione on cell cycle progression. A genome-scale correlation between DNA replication initiation and RNA transcription, which is equivalent to a recently discovered correlation and might be due to a previously unknown mechanism of regulation, is independently uncovered.