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Here we present a computational method, tensor-based imputation of gene-expression data at the single-cell level (TIGERS), which reveals the drug-induced single-cell transcriptomic landscape. With this algorithm, we predict missing drug-induced single-cell gene-expression data with tensor imputation, and identify trajectories of regulated pathways considering intercellular heterogeneity. Tensor imputation outperformed existing imputation methods for data completion, and provided cell-type-specific transcriptomic responses for unobserved drugs. For example, TIGERS correctly predicted the cell-type-specific expression of maker genes for pancreatic islets. Pathway trajectory analysis of the imputed gene-expression profiles of all combinations of drugs and human cells identified single-cell-specific drug activities and pathway trajectories that reflect drug-induced changes in pathway regulation. The proposed method is expected to expand our understanding of the single-cell mechanisms of drugs at the pathway level.<\/jats:p>","DOI":"10.1038\/s43588-022-00352-8","type":"journal-article","created":{"date-parts":[[2022,11,25]],"date-time":"2022-11-25T06:43:33Z","timestamp":1669358613000},"page":"758-770","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Pathway trajectory analysis with tensor imputation reveals drug-induced single-cell transcriptomic landscape"],"prefix":"10.1038","volume":"2","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6500-4692","authenticated-orcid":false,"given":"Michio","family":"Iwata","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroaki","family":"Mutsumine","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yusuke","family":"Nakayama","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Naomasa","family":"Suita","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2279-8773","authenticated-orcid":false,"given":"Yoshihiro","family":"Yamanishi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,11,24]]},"reference":[{"key":"352_CR1","doi-asserted-by":"publisher","first-page":"1929","DOI":"10.1126\/science.1132939","volume":"313","author":"J Lamb","year":"2006","unstructured":"Lamb, J. et al. 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