diff --git a/analyses/cell-type-ewings/references/README.md b/analyses/cell-type-ewings/references/README.md index 8dcd005e0..d0270e5da 100644 --- a/analyses/cell-type-ewings/references/README.md +++ b/analyses/cell-type-ewings/references/README.md @@ -62,9 +62,11 @@ The `gene_signatures` folder contains any custom gene lists obtained from public 1. `anyaud-ews-targets.tsv`: A list of the 78 marker genes defined by [Aynaud _et al._](https://doi.org/10.1016/j.celrep.2020.01.049) to be EWS-FLI1 targets. Figure 4 shows that expression of these targets is correlated with EWS-FLI1 levels at a single-cell level. +We expect these targets to have increased expression in cells with high EWS-FLI1 activity. 2. `wrenn-nt5e-genes.tsv`: A list of 28 genes from [Wrenn _et al._](https://doi.org/10.1158/1078-0432.CCR-23-1111) that represent the overlap between the top 217 genes correlated with _NT5E_ expression in patient tumors and the top 200 markers of _NT5E+_ Ewing sarcoma cells _in vitro_. -These genes are shown in Figure 5D and 5E. +These genes are shown in Figure 5D and 5E. +We expect these targets to have increased expression in cells with low EWS-FLI1 activity. The following gene sets from MSigDB were also used to define EWS-FLI1 targets and may be helpful in defining cell states: