Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data
Pseudotime algorithms can be employed to extract latent temporal information from cross-sectional data sets allowing dynamic biological processes to be studied in situations where the collection of time series data is challenging or prohibitive. Computational techniques have arisen from single-cell...
| Main Authors: | , |
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| Format: | Journal article |
| Language: | English |
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Nature Publishing Group
2017
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| _version_ | 1826288738845589504 |
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| author | Campbell, K Yau, C |
| author_facet | Campbell, K Yau, C |
| author_sort | Campbell, K |
| collection | OXFORD |
| description | Pseudotime algorithms can be employed to extract latent temporal information from cross-sectional data sets allowing dynamic biological processes to be studied in situations where the collection of time series data is challenging or prohibitive. Computational techniques have arisen from single-cell 'omics and cancer modelling where pseudotime can be used to learn about cellular differentiation or tumour progression. However, methods to date typically implicitly assume homogeneous genetic, phenotypic or environmental backgrounds, which becomes limiting as data sets grow in size and complexity. We describe a novel statistical framework that learns how pseudotime trajectories can be modulated through covariates that encode such factors. We apply this model to both single-cell and bulk gene expression data sets and show that the approach can recover known and novel covariate-pseudotime interaction effects. This hybrid regression-latent variable model framework extends pseudotemporal modelling from its most prevalent area of single cell genomics to wider applications. |
| first_indexed | 2024-03-07T02:18:14Z |
| format | Journal article |
| id | oxford-uuid:a3028cfd-376a-4a34-8eab-b0c977d9e657 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T02:18:14Z |
| publishDate | 2017 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | oxford-uuid:a3028cfd-376a-4a34-8eab-b0c977d9e6572022-03-27T02:23:50ZUncovering pseudotemporal trajectories with covariates from single cell and bulk expression dataJournal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:a3028cfd-376a-4a34-8eab-b0c977d9e657EnglishSymplectic Elements at OxfordNature Publishing Group2017Campbell, KYau, CPseudotime algorithms can be employed to extract latent temporal information from cross-sectional data sets allowing dynamic biological processes to be studied in situations where the collection of time series data is challenging or prohibitive. Computational techniques have arisen from single-cell 'omics and cancer modelling where pseudotime can be used to learn about cellular differentiation or tumour progression. However, methods to date typically implicitly assume homogeneous genetic, phenotypic or environmental backgrounds, which becomes limiting as data sets grow in size and complexity. We describe a novel statistical framework that learns how pseudotime trajectories can be modulated through covariates that encode such factors. We apply this model to both single-cell and bulk gene expression data sets and show that the approach can recover known and novel covariate-pseudotime interaction effects. This hybrid regression-latent variable model framework extends pseudotemporal modelling from its most prevalent area of single cell genomics to wider applications. |
| spellingShingle | Campbell, K Yau, C Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data |
| title | Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data |
| title_full | Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data |
| title_fullStr | Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data |
| title_full_unstemmed | Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data |
| title_short | Uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data |
| title_sort | uncovering pseudotemporal trajectories with covariates from single cell and bulk expression data |
| work_keys_str_mv | AT campbellk uncoveringpseudotemporaltrajectorieswithcovariatesfromsinglecellandbulkexpressiondata AT yauc uncoveringpseudotemporaltrajectorieswithcovariatesfromsinglecellandbulkexpressiondata |