Hyperbolic geometry of gene expression
Summary: Patterns of gene expressions play a key role in determining cell state. Although correlations in gene expressions have been well documented, most of the current methods treat them as independent variables. One way to take into account gene correlations is to find a low-dimensional curved ge...
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2021-03-01
|
| Series: | iScience |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2589004221001930 |
| _version_ | 1828896403900858368 |
|---|---|
| author | Yuansheng Zhou Tatyana O. Sharpee |
| author_facet | Yuansheng Zhou Tatyana O. Sharpee |
| author_sort | Yuansheng Zhou |
| collection | DOAJ |
| description | Summary: Patterns of gene expressions play a key role in determining cell state. Although correlations in gene expressions have been well documented, most of the current methods treat them as independent variables. One way to take into account gene correlations is to find a low-dimensional curved geometry that describes variation in the data. Here we develop such a method and find that gene expression across multiple cell types exhibits a low-dimensional hyperbolic structure. When more genes are taken into account, hyperbolic effects become stronger but representation remains low dimensional. The size of the hyperbolic map, which indicates the hierarchical depth of the data, was the largest for human cells, the smallest for mouse embryonic cells, and intermediate in differentiated cells from different mouse organs. We also describe how hyperbolic metric can be incorporated into the t-SNE method to improve visualizations compared with leading methods. |
| first_indexed | 2024-12-13T14:41:52Z |
| format | Article |
| id | doaj.art-0be56d57ad284b489787fd8f9e19ffe6 |
| institution | Directory Open Access Journal |
| issn | 2589-0042 |
| language | English |
| last_indexed | 2024-12-13T14:41:52Z |
| publishDate | 2021-03-01 |
| publisher | Elsevier |
| record_format | Article |
| series | iScience |
| spelling | doaj.art-0be56d57ad284b489787fd8f9e19ffe62022-12-21T23:41:35ZengElsevieriScience2589-00422021-03-01243102225Hyperbolic geometry of gene expressionYuansheng Zhou0Tatyana O. Sharpee1Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USAComputational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, CA 92037, USA; Department of Physics, University of California San Diego, La Jolla, CA 92093, USA; Corresponding authorSummary: Patterns of gene expressions play a key role in determining cell state. Although correlations in gene expressions have been well documented, most of the current methods treat them as independent variables. One way to take into account gene correlations is to find a low-dimensional curved geometry that describes variation in the data. Here we develop such a method and find that gene expression across multiple cell types exhibits a low-dimensional hyperbolic structure. When more genes are taken into account, hyperbolic effects become stronger but representation remains low dimensional. The size of the hyperbolic map, which indicates the hierarchical depth of the data, was the largest for human cells, the smallest for mouse embryonic cells, and intermediate in differentiated cells from different mouse organs. We also describe how hyperbolic metric can be incorporated into the t-SNE method to improve visualizations compared with leading methods.http://www.sciencedirect.com/science/article/pii/S2589004221001930GenesCell BiologyComplex Systems |
| spellingShingle | Yuansheng Zhou Tatyana O. Sharpee Hyperbolic geometry of gene expression iScience Genes Cell Biology Complex Systems |
| title | Hyperbolic geometry of gene expression |
| title_full | Hyperbolic geometry of gene expression |
| title_fullStr | Hyperbolic geometry of gene expression |
| title_full_unstemmed | Hyperbolic geometry of gene expression |
| title_short | Hyperbolic geometry of gene expression |
| title_sort | hyperbolic geometry of gene expression |
| topic | Genes Cell Biology Complex Systems |
| url | http://www.sciencedirect.com/science/article/pii/S2589004221001930 |
| work_keys_str_mv | AT yuanshengzhou hyperbolicgeometryofgeneexpression AT tatyanaosharpee hyperbolicgeometryofgeneexpression |