ArticleProceedings of the National Academy of Sciences of the United States of America2007
A tensor higher-order singular value decomposition for integrative analysis of DNA microarray data from different studies.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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41 citing papers in PubMed.
- The structure is the message: Preserving experimental context through tensor decomposition.Cell systems · 2024Review
- Stable tensor neural networks for efficient deep learning.Frontiers in big data · 2024Article
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- Context-aware deconvolution of cell-cell communication with Tensor-cell2cell.Nature communications · 2022Article
- Degree of Freedom of Gene Expression in Saccharomyces cerevisiae.Microbiology spectrum · 2022Article
- Frataxin Deficit Leads to Reduced Dynamics of Growth Cones in Dorsal Root Ganglia Neurons of Friedreich's Ataxia YG8sR Model: A Multilinear Algebra Approach.Frontiers in molecular neuroscience · 2022Article
- Tensor-structured decomposition improves systems serology analysis.Molecular systems biology · 2021Article
- Stimulus-specificity in the Responses of Immune Sentinel Cells.Current opinion in systems biology · 2019Article
- Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization.Nucleic acids research · 2019Article
- Orthogonal joint sparse NMF for microarray data analysis.Journal of mathematical biology · 2019Article
- THREE-WAY CLUSTERING OF MULTI-TISSUE MULTI-INDIVIDUAL GENE EXPRESSION DATA USING SEMI-NONNEGATIVE TENSOR DECOMPOSITION.The annals of applied statistics · 2019Article
- Tightly integrated genomic and epigenomic data mining using tensor decomposition.Bioinformatics (Oxford, England) · 2019Article
- Article
- Identifying gene-gene interactions using penalized tensor regression.Statistics in medicine · 2018Article
- OPERATOR NORM INEQUALITIES BETWEEN TENSOR UNFOLDINGS ON THE PARTITION LATTICE.Linear algebra and its applications · 2017Article
- Tensor factorization toward precision medicine.Briefings in bioinformatics · 2017Article
- Navigating the Functional Landscape of Transcription Factors via Non-Negative Tensor Factorization Analysis of MEDLINE Abstracts.Frontiers in bioengineering and biotechnology · 2017Article
- Tensor decomposition-based unsupervised feature extraction applied to matrix products for multi-view data processing.PloS one · 2017Article
- Community ecology in 3D: Tensor decomposition reveals spatio-temporal dynamics of large ecological communities.PloS one · 2017Article
- TNF-insulin crosstalk at the transcription factor GATA6 is revealed by a model that links signaling and transcriptomic data tensors.Science signaling · 2016Article
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3 authors.
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Abstract
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.
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