Additional file 2 of Dissection of multiple sclerosis genetics identifies B and CD4+ T cells as driver cell subsets
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- Guo, Michael H.; Sama, Prashanth; LaBarre, Brenna A.; Lokhande, Hrishikesh; Balibalos, John; Chu, Ci; Du, Xiaomi; Kheradpour, Pouya; Kim, Charles C.; Oniskey, Taylor; Snyder, Thomas; Soghoian, Damien Z.; Weiner, Howard L.; Chitnis, Tanuja; Patsopoulos, Nikolaos A.
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Additional file 2: Supplementary Figures. Figure S1. Correlation in ATAC-seq profiles across hematopoietic cell types. Figure S2. LDSC enrichments for MS GWAS in cell-type specific ATAC-seq peaks mature hematopoietic cell type. Figure S3. Enrichments of GWAS results from 10 neuropsychiatric or autoimmune conditions in OCRs across various hematopoietic cell types. Figure S4. LDSC results for MS GWAS in ATAC-seq peaks from treated MS patients. Figure S5. LDSC results for MS GWAS in histone ChIP-seq. Figure S6. LDSC results for MS GWAS in chromHMM partitions. Figure S7. Distribution of credible set variants. Figure S8. Number of GWAS loci with ATAC-seq peak overlapping fine-mapped SNP. Figure S9. Colocalization of MS GWAS loci with DICE CD4 T and B cell eQTLs. Figure S10. Colocalization enrichment of MS GWAS loci with DICE CD4 T and B cell eQTLs. Figure S11. Protein-protein interaction communities of putative causal genes in CD4 T cells. Figure S12. Protein-protein interaction communities of putative causal genes in B cells. Figure S13. Protein-protein interaction communities of putative causal genes shared in CD4 T and B cells. Figure S14. Protein-protein interaction communities of putative causal genes unique in CD4 T cells. Figure S15. Protein-protein interaction communities of putative causal genes unique in B cells. Figure S16. Enrichment of CD4 T cell putative causal genes in GTRD database. Figure S17. Enrichment of B cell putative causal genes in GTRD database. Figure S18. Enrichment of shared between CD4 T and B cells putative causal genes in GTRD database. Figure S19. Change of gene expression of CD4 T cell putative causal genes in knock-down (KD) and over-expression (OE) models in cancer cell lines. Figure S20. Change of gene expression of B cell putative causal genes in knock-down (KD) and over-expression (OE) models in cancer cell lines.