Merge remote-tracking branch 'AlexsLemonade/main' into allyhawkins/bu…

…ild-consensus-reference

analyses/cell-type-ewings/references/README.md

@@ -49,3 +49,38 @@ The other required input for `InferCNV` is an annotation file with two columns a
 The first column contains the cell barcode and the second contains the annotation for that cell (either `reference` or `unknown`).
 These files are specific for each library and depend on which cells are denoted as the reference.
 Each library contains a folder with any annotations file used to run `InferCNV` for that library.
+
+## Marker gene sets for identifying tumor cell states 
+
+The `tumor-cell-state-markers.tsv` file contains a list of marker genes that can be used to classify tumor cell states in Ewing samples. 
+The marker genes included here are specific to EWS-FLI1 high, EWS-FLI1 low, and proliferative tumor cells. 
+This list was obtained based on key genes mentioned in [Goodspeed _et al._](https://doi.org/10.1101/2024.01.18.576251), [Aynaud _et al._](https://doi.org/10.1016/j.celrep.2020.01.049), and [Wrenn _et al._](https://doi.org/10.1158/1078-0432.CCR-23-1111). 
+
+### Gene signatures 
+
+The `gene_signatures` folder contains any custom gene lists obtained from publications that can be used to identify tumor cell states: 
+
+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.
+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:  
+
+- [STAEGE_EWING_FAMILY_TUMOR](https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/STAEGE_EWING_FAMILY_TUMOR.html)
+- [MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP](https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP.html)
+- [MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN](https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN.html)
+- [ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION](https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION.html)
+- [RIGGI_EWING_SARCOMA_PROGENITOR_UP](https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/RIGGI_EWING_SARCOMA_PROGENITOR_UP.html) 
+- [RIGGI_EWING_SARCOMA_PROGENITOR_DN](https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/RIGGI_EWING_SARCOMA_PROGENITOR_DN.html) 
+- [KINSEY_TARGETS_OF_EWSR1_FLI1_FUSION_UP](https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP.html)
+- [KINSEY_TARGETS_OF_EWSR1_FLI1_FUSION_DN](https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN.html)
+
+Wrenn _et al._ also used found that the following additional gene sets were highly expressed in CD73 high, EWS-FLI1 low tumor cells: 
+
+- [HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION](https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION.html)
+GO:BP ECM Organization 
+- [GOBP_REGULATION_OF_EXTRACELLULAR_MATRIX_ORGANIZATION](https://www.gsea-msigdb.org/gsea/msigdb/human/geneset/GOBP_REGULATION_OF_EXTRACELLULAR_MATRIX_ORGANIZATION.html)

analyses/cell-type-ewings/references/gene_signatures/aynaud-ews-targets.tsv

@@ -0,0 +1,79 @@
+gene_symbol	ensembl_gene_id
+CAV1	ENSG00000105974
+APCDD1	ENSG00000154856
+CCND1	ENSG00000110092
+RNF141	ENSG00000110315
+RBM11	ENSG00000185272
+TSPAN13	ENSG00000106537
+FZD1	ENSG00000157240
+RCOR1	ENSG00000089902
+ATP1A1	ENSG00000163399
+TMEM47	ENSG00000147027
+GLCE	ENSG00000138604
+LIPI	ENSG00000188992
+RP13-16H11.2	NA
+CLDN1	ENSG00000163347
+PAX9	ENSG00000198807
+TNFAIP6	ENSG00000123610
+UGT3A2	ENSG00000168671
+GPR64	NA
+SLAIN1	ENSG00000139737
+RP11-1258F18.1	NA
+MARCH1	NA
+AASS	ENSG00000008311
+ABHD6	ENSG00000163686
+AC022311.1	NA
+ADAMTS4	ENSG00000158859
+AK3	ENSG00000147853
+AKAP7	ENSG00000118507
+CDH8	ENSG00000150394
+CES1	ENSG00000198848
+COL21A1	ENSG00000124749
+CTTNBP2	ENSG00000077063
+ATP11C	ENSG00000101974
+BARX2	ENSG00000043039
+CACHD1	ENSG00000158966
+CADPS2	ENSG00000081803
+CAPRIN1	ENSG00000135387
+CAV2	ENSG00000105971
+CDC37L1	ENSG00000106993
+DCC	ENSG00000187323
+DCDC2	ENSG00000146038
+DLGAP1	ENSG00000170579
+DNAL4	ENSG00000100246
+EBF3	ENSG00000108001
+ENPP1	ENSG00000197594
+FAM46A	NA
+FAM49A	NA
+FNBP1	ENSG00000187239
+FOS	ENSG00000170345
+HES1	ENSG00000114315
+HMCN1	ENSG00000143341
+IGF1	ENSG00000017427
+JARID2	ENSG00000008083
+KCNE4	ENSG00000152049
+KDSR	ENSG00000119537
+KIAA1456	NA
+KIAA1462	NA
+KIT	ENSG00000157404
+LRRC4C	ENSG00000148948
+MAN2A1	ENSG00000112893
+MLLT3	ENSG00000171843
+MYC	ENSG00000136997
+NMI	ENSG00000123609
+NPTXR	ENSG00000221890
+NTNG1	ENSG00000162631
+PCDH7	ENSG00000169851
+PCSK2	ENSG00000125851
+PRKCB	ENSG00000166501
+RP11-521M14.1	NA
+RP11-6C14.1	NA
+RP13-16H11.1	NA
+SH2B3	ENSG00000111252
+SH3PXD2A	ENSG00000107957
+SLC26A2	ENSG00000155850
+SLCO5A1	ENSG00000137571
+SPATA6L	ENSG00000106686
+TRAV1-2	ENSG00000256553
+TRPM4	ENSG00000130529
+ZC3H13	ENSG00000123200

analyses/cell-type-ewings/references/gene_signatures/wrenn-nt5e-genes.tsv

@@ -0,0 +1,29 @@
+gene_symbol	ensembl_gene_id
+NT5E	ENSG00000135318
+FBN1	ENSG00000166147
+COL5A2	ENSG00000204262
+COL6A2	ENSG00000142173
+TNC	ENSG00000041982
+COL1A1	ENSG00000108821
+COL1A2	ENSG00000164692
+SPARC	ENSG00000113140
+BGN	ENSG00000182492
+S100A10	ENSG00000197747
+FSTL1	ENSG00000163430
+CAMK2D	ENSG00000145349
+CTSB	ENSG00000164733
+THY1	ENSG00000154096
+GPNMB	ENSG00000136235
+NID1	ENSG00000116962
+PPIC	ENSG00000168938
+PRSS23	ENSG00000150687
+EMP1	ENSG00000134531
+CD63	ENSG00000135404
+S100A11	ENSG00000163191
+LGMN	ENSG00000100600
+S100A13	ENSG00000189171
+S100A4	ENSG00000196154
+MYOF	ENSG00000138119
+PLAC9	ENSG00000189129
+TGFB1I1	ENSG00000140682
+CTSZ	ENSG00000101160

analyses/cell-type-ewings/references/tumor-cell-state-markers.tsv

@@ -0,0 +1,19 @@
+cell_state	gene_symbol	ensembl_gene_id	source
+proliferative	MKI67	ENSG00000148773	https://doi.org/10.1101/2024.01.18.576251;https://doi.org/10.1158/1078-0432.CCR-23-1111
+proliferative	PCNA	ENSG00000132646	https://doi.org/10.1101/2024.01.18.576251
+EWS-low	NT5E	ENSG00000135318	https://doi.org/10.1158/1078-0432.CCR-23-1111
+EWS-low	IGFBP3	ENSG00000146674	https://doi.org/10.1016/j.celrep.2020.01.049
+EWS-low	IL8	ENSG00000169429	https://doi.org/10.1016/j.celrep.2020.01.049
+EWS-low	LOX	ENSG00000113083	https://doi.org/10.1016/j.celrep.2020.01.049
+EWS-low	VIM	ENSG00000026025	https://doi.org/10.1016/j.celrep.2020.01.049
+EWS-low	TNC	ENSG00000041982	https://doi.org/10.1158/1078-0432.CCR-23-1111
+EWS-low	COL1A1	ENSG00000108821	https://doi.org/10.1158/1078-0432.CCR-23-1111
+EWS-low	BGN	ENSG00000182492	https://doi.org/10.1158/1078-0432.CCR-23-1111
+EWS-low	S100A10	ENSG00000197747	https://doi.org/10.1158/1078-0432.CCR-23-1111
+EWS-low	SPARC	ENSG00000113140	https://doi.org/10.1158/1078-0432.CCR-23-1111
+EWS-low	COL1A2	ENSG00000164692	https://doi.org/10.1158/1078-0432.CCR-23-1111
+EWS-low	CD44	ENSG00000026508	https://doi.org/10.1101/2024.01.18.576251
+EWS-high	PRKCB	ENSG00000166501	https://doi.org/10.1016/j.celrep.2020.01.049
+EWS-high	LIPI	ENSG00000188992	https://doi.org/10.1016/j.celrep.2020.01.049
+EWS-high	CCND1	ENSG00000110092	https://doi.org/10.1016/j.celrep.2020.01.049
+EWS-high	NR0B1	ENSG00000169297	https://doi.org/10.1016/j.celrep.2020.01.049