Marker Catalog
Compiled: 2022-03-17
Marker_Catalog.RmdCell-type markers
Marker-based cell-type annotation requires a reference databse comprised of cell-type annotated gene sets. To generate a cell-type marker reference catalog, we derived cell-type markers from public diverse scRNAseq atlases and using the Wilcoxon DE method to identify differentially-expressed genes across author-curated cell types. All markers satisfying logFC > 0.5, AUROC > 0.95 and FDR < 1% were included. If less than 15 markers were identified per a cell-type using these criteria, the top N markers (ranked by logFC) that satisfied FDR < 1% were taken to ensure the minimum 15 markers per cell-type requirement was satisfied.
Cell-type marker catalog
Table of cell-type markers
# load markers (loaded as data.frame)
cell_catalog <- geneSets[["Cell_Catalog"]]
# list representation as follows:
cell_catalog.list <- wideDF2namedList(cell_catalog)
# show table
flex.asDT(cell_catalog, page_length = 10, scrollX = TRUE)Represented cell-types
Here is a cell-type look up table to check cell-type representation in our catalog.
# show cell-types
flex.asDT(data.frame(cell_types = names(cell_catalog.list)), page_length = 10)Single cell atlases
Here are the annotated atlases that were used to derive our marker catalog:
Cao 2019 | Murine Organogenesis
Cao, J., Spielmann, M., Qiu, X., Huang, X., Ibrahim, D. M., Hill, A. J., . . . Steemers, F. J. (2019). The single-cell transcriptional landscape of mammalian organogenesis. Nature, 566(7745), 496-502. link
Cao 2020 | Human Fetus
Cao, J., O’Day, D. R., Pliner, H. A., Kingsley, P. D., Deng, M., Daza, R. M., . . . Zhang, F. (2020). A human cell atlas of fetal gene expression. Science, 370(6518). link
La Manno 2021 | Developing Murine Brain
La Manno, G., Siletti, K., Furlan, A., Gyllborg, D., Vinsland, E., Mossi Albiach, A., . . . Dratva, L. M. (2021). Molecular architecture of the developing mouse brain. Nature, 596(7870), 92-96. link
Pijuan-Sala 2019 | Murine Gastrulation
Pijuan-Sala, B., Griffiths, J. A., Guibentif, C., Hiscock, T. W., Jawaid, W., Calero-Nieto, F. J., . . . Ho, D. L. L. (2019). A single-cell molecular map of mouse gastrulation and early organogenesis. Nature, 566(7745), 490-495. link
Tabula Muris | Murine Cell-Type Atlas
Consortium, T. M. (2018). Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris. Nature, 562(7727), 367-372. link
Tabula Sapiens | Human Cell-Type Atlas
Quake, S. R., & Consortium, T. S. (2021). The Tabula Sapiens: a single cell transcriptomic atlas of multiple organs from individual human donors. Biorxiv. link
Tyser 2021 | Human Gastrulation
Tyser, R. C., Mahammadov, E., Nakanoh, S., Vallier, L., Scialdone, A., & Srinivas, S. (2021). Single-cell transcriptomic characterization of a gastrulating human embryo. Nature, 1-5. link
Zeisel 2018 | Adolescent Murine Brain
Zeisel, A., Hochgerner, H., Lönnerberg, P., Johnsson, A., Memic, F., Van Der Zwan, J., . . . La Manno, G. (2018). Molecular architecture of the mouse nervous system. Cell, 174(4), 999-1014. e1022. link
Other cell-type databases
There are other cell-type marker databases available, including PanglaoDB, CellMarkers and MSigDB
We have consolidated the cell-type markers from PanglaoDB and CellMarkers, and they can be accessed as follows:
PanglaoDB
# load markers
murine_markers <- geneSets[["Panglao_Mm"]]
human_markers <- geneSets[["Panglao_Hs"]]
flex.asDT(human_markers, page_length = 10, scrollX = TRUE)CellMarkers
# load markers
cell_markers <- geneSets[["CellMarker_Hs_Zhang2019"]]
flex.asDT(cell_markers, page_length = 10, scrollX = TRUE)Session Info
## R version 4.0.3 (2020-10-10)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## Running under: Windows 10 x64 (build 19041)
##
## Matrix products: default
##
## locale:
## [1] LC_COLLATE=English_Canada.1252 LC_CTYPE=English_Canada.1252
## [3] LC_MONETARY=English_Canada.1252 LC_NUMERIC=C
## [5] LC_TIME=English_Canada.1252
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] DT_0.19 scMiko_0.1.0 flexdashboard_0.5.2
## [4] tidyr_1.1.3 SeuratObject_4.0.4 Seurat_4.1.0
## [7] dplyr_1.0.7 ggplot2_3.3.5
##
## loaded via a namespace (and not attached):
## [1] Rtsne_0.15 colorspace_2.0-2 deldir_0.2-10
## [4] ellipsis_0.3.2 ggridges_0.5.3 rprojroot_2.0.2
## [7] fs_1.5.0 spatstat.data_2.1-0 leiden_0.3.9
## [10] listenv_0.8.0 ggrepel_0.9.1 fansi_0.5.0
## [13] codetools_0.2-16 splines_4.0.3 cachem_1.0.6
## [16] knitr_1.36 polyclip_1.10-0 jsonlite_1.7.2
## [19] ica_1.0-2 cluster_2.1.0 png_0.1-7
## [22] uwot_0.1.10 spatstat.sparse_2.0-0 shiny_1.6.0
## [25] sctransform_0.3.3 compiler_4.0.3 httr_1.4.2
## [28] assertthat_0.2.1 Matrix_1.3-4 fastmap_1.1.0
## [31] lazyeval_0.2.2 later_1.3.0 formatR_1.11
## [34] htmltools_0.5.2 tools_4.0.3 igraph_1.2.6
## [37] gtable_0.3.0 glue_1.4.2 RANN_2.6.1
## [40] reshape2_1.4.4 Rcpp_1.0.7 scattermore_0.7
## [43] jquerylib_0.1.4 pkgdown_1.6.1 vctrs_0.3.8
## [46] nlme_3.1-149 crosstalk_1.1.1 lmtest_0.9-38
## [49] xfun_0.26 stringr_1.4.0 globals_0.14.0
## [52] mime_0.11 miniUI_0.1.1.1 lifecycle_1.0.1
## [55] irlba_2.3.3 goftest_1.2-2 future_1.22.1
## [58] MASS_7.3-53 zoo_1.8-9 scales_1.1.1
## [61] spatstat.core_2.3-0 ragg_1.1.3 promises_1.2.0.1
## [64] spatstat.utils_2.2-0 parallel_4.0.3 RColorBrewer_1.1-2
## [67] yaml_2.2.1 memoise_2.0.0 reticulate_1.20
## [70] pbapply_1.5-0 gridExtra_2.3 sass_0.4.0
## [73] rpart_4.1-15 stringi_1.7.4 highr_0.9
## [76] desc_1.3.0 rlang_0.4.11 pkgconfig_2.0.3
## [79] systemfonts_1.0.2 matrixStats_0.61.0 evaluate_0.14
## [82] lattice_0.20-41 tensor_1.5 ROCR_1.0-11
## [85] purrr_0.3.4 patchwork_1.1.1 htmlwidgets_1.5.4
## [88] cowplot_1.1.1 tidyselect_1.1.1 parallelly_1.28.1
## [91] RcppAnnoy_0.0.19 plyr_1.8.6 magrittr_2.0.1
## [94] R6_2.5.1 generics_0.1.0 DBI_1.1.1
## [97] mgcv_1.8-33 pillar_1.6.4 withr_2.4.2
## [100] fitdistrplus_1.1-5 abind_1.4-5 survival_3.2-13
## [103] tibble_3.1.4 future.apply_1.8.1 crayon_1.4.1
## [106] KernSmooth_2.23-17 utf8_1.2.2 spatstat.geom_2.2-2
## [109] plotly_4.9.4.1 rmarkdown_2.11 grid_4.0.3
## [112] data.table_1.14.0 digest_0.6.27 xtable_1.8-4
## [115] httpuv_1.6.3 textshaping_0.3.5 munsell_0.5.0
## [118] viridisLite_0.4.0 bslib_0.3.0