Additional file 16: of CellMapper: rapid and accurate inference of gene expression in difficult-to-isolate cell types
Year: 2016
Type: article
Abstract: Robustness of CellMapper to query gene choice; companion figure to Fig. 2a. To test the sensitivity of CellMapper to the choice of query gene, we repeated our analysis for the three neuron subtypes and NG2 glia using each of the classic cell markers (positive controls) as query genes. Dot charts display the rank of the non-query gene classic markers within CellMapper’s predictions for each cell type. Dots are colored based on their known primary cell type of expression. Dark gray shading covers the area (rank list) required to identify all positive control genes for each cell type. Genes with promoters that have been used to drive cell-specific expression in mice (i.e. cell-specific reporter mouse strains available from cre.jax.org) are highlighted in bold with an asterisk under the “Query Gene” column. These genes have well-established expression patterns in the selected cell type and generally performed well as query genes. Many of the other classic cell markers have alternative sites of expression and were less effective as query genes. For instance, SLC18A2 is expressed strongly in both serotonergic and noradrenergic neurons and returned markers expressed in both cell types. Factors to consider when choosing query genes for other cell types are described in the CellMapper R Package vignette ( http://bioconductor.org/packages/CellMapper/ ). (PDF 69 kb)
Source: Figshare
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W7138384886