MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics
Abstract Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-om...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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BMC
2017-07-01
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| Series: | Genome Biology |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s13059-017-1269-0 |
| _version_ | 1818777227634933760 |
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| author | Joshua D. Welch Alexander J. Hartemink Jan F. Prins |
| author_facet | Joshua D. Welch Alexander J. Hartemink Jan F. Prins |
| author_sort | Joshua D. Welch |
| collection | DOAJ |
| description | Abstract Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-omic profiles from transcriptomic and epigenetic measurements performed on different cells of the same type. Using scM&T-seq and sc-GEM data, we confirm that MATCHER accurately predicts true single cell correlations between DNA methylation and gene expression without using known cell correspondences. MATCHER also reveals new insights into the dynamic interplay between the transcriptome and epigenome in single embryonic stem cells and induced pluripotent stem cells. |
| first_indexed | 2024-12-18T11:25:29Z |
| format | Article |
| id | doaj.art-71449ce294ab45cd8643b94b03412705 |
| institution | Directory Open Access Journal |
| issn | 1474-760X |
| language | English |
| last_indexed | 2024-12-18T11:25:29Z |
| publishDate | 2017-07-01 |
| publisher | BMC |
| record_format | Article |
| series | Genome Biology |
| spelling | doaj.art-71449ce294ab45cd8643b94b034127052022-12-21T21:09:42ZengBMCGenome Biology1474-760X2017-07-0118111910.1186/s13059-017-1269-0MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamicsJoshua D. Welch0Alexander J. Hartemink1Jan F. Prins2Department of Computer Science, The University of North Carolina at Chapel HillDepartment of Computer Science, Duke UniversityDepartment of Computer Science, The University of North Carolina at Chapel HillAbstract Single cell experimental techniques reveal transcriptomic and epigenetic heterogeneity among cells, but how these are related is unclear. We present MATCHER, an approach for integrating multiple types of single cell measurements. MATCHER uses manifold alignment to infer single cell multi-omic profiles from transcriptomic and epigenetic measurements performed on different cells of the same type. Using scM&T-seq and sc-GEM data, we confirm that MATCHER accurately predicts true single cell correlations between DNA methylation and gene expression without using known cell correspondences. MATCHER also reveals new insights into the dynamic interplay between the transcriptome and epigenome in single embryonic stem cells and induced pluripotent stem cells.http://link.springer.com/article/10.1186/s13059-017-1269-0Single cell RNA-seqSingle cell epigenomicsManifold learningManifold alignment |
| spellingShingle | Joshua D. Welch Alexander J. Hartemink Jan F. Prins MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics Genome Biology Single cell RNA-seq Single cell epigenomics Manifold learning Manifold alignment |
| title | MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics |
| title_full | MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics |
| title_fullStr | MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics |
| title_full_unstemmed | MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics |
| title_short | MATCHER: manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics |
| title_sort | matcher manifold alignment reveals correspondence between single cell transcriptome and epigenome dynamics |
| topic | Single cell RNA-seq Single cell epigenomics Manifold learning Manifold alignment |
| url | http://link.springer.com/article/10.1186/s13059-017-1269-0 |
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