At a glance
RTE quantification and cell type annotation
In scARE, we offer quantification of retrotransposable elements (RTEs) and genes for each included dataset. Cell annotations were conducted by referencing the Allen Brain Atlas, and clustering was performed based on gene/RTE expression levels.
Discovering most expressed and most differential expressed RTEs
In scARE, we offer discovery options for exploring the most highly expressed RTEs and the most differentially expressed RTEs.
Explore expression of RTE in cell types
In scARE, we summarize the expression profiles of retrotransposable elements (RTEs) in each cell type, enabling exploration of RTE expression across various cell types.
Discovering co-expression of RTE and gene
In scARE, we conducted co-expression analysis between retrotransposable elements (RTEs) and genes, facilitating the discovery of correlations between genes and RTEs.
About
In scARE, we compiled scRNA-seq dataset from 12 studies in Alzheimer’s disease, Parkinson’s disease, and multiple sclerosis, to reveal RTE dynamics in disease and cell types. In total, we quantified RTE expression in more than 600,000 cells and built a single cell atlas of retrotransposable elements (scARE) to host these data. We also provide various search and browse options, including searching for RTEs, genes, diseases or datasets by single term and multiple terms, browse by RTE, cell type, disease, and dataset. Furthermore, we implemented a discover option to highlight most expressed, differential expressed or co-expressed RTEs under given conditions.
Developer
Wankun Deng (Website maintainer)
Citu (Data source maintainer)
Andi Liu (Data source maintainer)
Zhongming Zhao (Mentor)
Citation
Deng W*, Citu*, Liu A, Zhao Z#. Dynamic dysregulation of retrotransposons in neurodegenerative diseases at single-cell level. Preparing.