--- title: UMAP Construction slug: umap-construction createdAt: 2026-04-28T11:58:47.173Z --- UMAP dimensionality reduction projects high-dimensional single-cell expression profiles into a low-dimensional space that preserves both local and global transcriptional relationships. This enables visualization of cellular heterogeneity and highlights context-specific gene expression at cell type resolution. The plots were generated from one representative dataset from the CZ CELLxGENE-collection (1,2), corresponding to the same tissue type as the displayed network. To reduce loading time within Mavatar Discovery, large datasets (more than approximately 50,000 cells) were subsetted, while ensuring that the subset remained representative and that all cell types were retained. For UMAP visualization, the raw expression data were normalized and scaled to zero mean and unit variance. Normalized, unscaled data were used for the violin plots. *Table 1. Information on the datasets used for UMAPs and Violin plots, for the different networks within Mavatar Discovery.* | Tissue | Collection | Dataset | Source plot | | ---------------- | ---------------------------------------------------------------------------------------------------------------------- | ---------------- | --------------------------------------------------------------------------------------- | | Blood/PBMC | Tabula Sapiens | Blood | [Explore](https://cellxgene.cziscience.com/e/983d5ec9-40e8-4512-9e65-a572a9c486cb.cxg/) | | Bone marrow | Tabula Sapiens | Bone\_Marrow | [Explore](https://cellxgene.cziscience.com/e/4f1555bc-4664-46c3-a606-78d34dd10d92.cxg/) | | Brain | Human Brain Cell Atlas v1.0 | All neurons | [Explore](https://cellxgene.cziscience.com/e/6ed0bb6c-a9e3-4ba6-9436-7c8fd4e206f0.cxg/) | | Breast | Human Breast Cancer Single Cell Atlas | Global Atlas | [Explore](https://cellxgene.cziscience.com/e/de5416ef-bbfa-41f3-99d4-01a3554173f5.cxg/) | | Gastrointestinal | A proximal-to-distal survey of healthy adult human small intestine and colon epithelium by single-cell transcriptomics | | [Explore](https://cellxgene.cziscience.com/e/019c7af2-c827-4454-9970-44d5e39ce068.cxg/) | | Large intestine | Tabula Sapiens | Large\_Intestine | [Explore](https://cellxgene.cziscience.com/e/7357cee7-9f7f-4ab0-8cec-90de8f047e38.cxg/) | | Liver | Tabula Sapiens | Liver | [Explore](https://cellxgene.cziscience.com/e/6d41668c-168c-4500-b06a-4674ccf3e19d.cxg/) | | Lung | Tabula Sapiens | Lung | [Explore](https://cellxgene.cziscience.com/e/0d2ee4ac-05ee-40b2-afb6-ebb584caa867.cxg/) | | Multi-tissue | Tabula Sapiens | Immune | [Explore](https://cellxgene.cziscience.com/e/c5d88abe-f23a-45fa-a534-788985e93dad.cxg/) | | Ovary | Tabula Sapiens | Ovary | [Explore](https://cellxgene.cziscience.com/e/bb78adbb-1428-4468-bad0-63602bb974e9.cxg/) | | Pancreas | Automatic cell-type harmonization and integration across Human Cell Atlas datasets | Pancreas | [Explore](https://cellxgene.cziscience.com/e/31f657dc-1875-4c4b-a5ca-ce63b3ef3a82.cxg/) | | Prostate | Tabula Sapiens | Prostate | [Explore](https://cellxgene.cziscience.com/e/d77ec7d6-ef2e-49d6-9e79-05b7f8881484.cxg/) | | Skin | Tabula Sapiens | Skin | [Explore](https://cellxgene.cziscience.com/e/0041b9c3-6a49-4bf7-8514-9bc7190067a7.cxg/) | | Small intestine | Tabula Sapiens | Small\_Intestine | [Explore](https://cellxgene.cziscience.com/e/a357414d-2042-4eb5-95f0-c58604a18bdd.cxg/) | | | | | | Read more on how to interpret the UMAP in Mavatar Discovery under [Cell Type Explorer](docId\:XFU1ggaWGnttLn4ypFW0V). # References 1. S. Abdulla, B. Aevermann, P. Assis, S. Badajoz, S. M. Bell, E. Bezzi, B. Cakir, J. Chaffer, S. Chambers, J. M. Cherry, T. Chi, J. Chien, L. Dorman, P. Garcia-Nieto, N. Gloria, M. Hastie, D. Hegeman, J. Hilton, T. Huang, A. Infeld, A.-M. Istrate, I. Jelic, K. Katsuya, Y. J. Kim, K. Liang, M. Lin, M. Lombardo, B. Marshall, B. Martin, F. Mcdade, C. Megill, N. Patel, A. Predeus, B. Raymor, B. Robatmili, D. Rogers, E. Rutherford, D. Sadgat, A. Shin, C. Small, T. Smith, P. Sridharan, A. Tarashansky, N. Tavares, H. Thomas, A. Tolopko, M. Urisko, J. Yan, G. Yeretssian, J. Zamanian, A. Mani, J. Cool, A. Carr, C. Zuckerberg Initiative, C. Z. Biohub, CZ CELL×GENE Discover: A single-cell data platform for scalable exploration, analysis and modeling of aggregated data. *bioRxiv*, 2023.10.30.563174 (2023). [https://www.biorxiv.org/content/10.1101/2023.10.30.563174v1](https://www.biorxiv.org/content/10.1101/2023.10.30.563174v1) 2. CZ CELLxGENE Discover - Cellular Visualization Tool (available at [https://cellxgene.cziscience.com/](https://cellxgene.cziscience.com/))