DOI: 10.5281/zenodo.4715907
title: MyND RNAseq and eQTL results

description: This dataset is part of the manuscript: "Dysregulation of mitochondrial and proteo-lysosomal genes in Parkinson's disease myeloid cells", by Navarro E, Udine E, et al. <strong>Description of files:</strong> <em>MyND_monocyte.cis_eqtl_nominal.txt.gz</em> - Full <strong>nominal eQTL</strong> summary statistics (gzip-compressed) <em>MyND_monocyte.cis_eqtl_permuted.txt.gz</em> - Full <strong>permuted eQTL</strong> summary statistics (gzip-compressed) <em>MyND_monocyte.cis_sqtl_nominal.txt.gz</em> - Full <strong>nominal sQTL</strong> summary statistics (gzip-compressed) <em>MyND_monocyte.cis_sqtl_permuted.txt.gz</em> - Full <strong>permuted sQTL</strong> summary statistics (gzip-compressed) <em>gencode.v30.primary_assembly.annotation.txt.gz</em> - Gencode (v30) gene annotations used in the analysis (gzip-compressed) <em>monocyte_counts_matrix.txt.gz</em> - RSEM counts from <strong>monocytes</strong> samples (230 samples) (gzip-compressed) <em>monocyte_tpms_matrix.txt.gz </em>-RSEM TPMs from <strong>monocytes</strong> samples (230 samples) (gzip-compressed) <em>microglia_counts_matrix.txt.gz</em> - RSEM counts from <strong>microglia</strong> samples (128 samples - 55 donors) (gzip-compressed) <em>microglia_tpms_matrix.txt.gz</em> - RSEM TPMs from <strong>microglia</strong> samples (128 samples - 55 donors) (gzip-compressed) <em>processed_seurat_obj.RDS</em> - Seurat R data object file containing <strong>single-cell RNA-seq</strong> results (14,827 features, 19,144 cells, 10 donors) <strong>Table columns are formatted as follows:</strong> <strong>Nominal eQTL</strong> results include all SNP-gene pairs tested (using a 1Mb window from each side of the transcription start site (TSS) of a gene). Table columns are formatted as follows: "pheno_id" - The phenotype ID "pheno_chr" - The chromosome ID of the phenotype "pheno_start" - The start position of the phenotype "pheno_end" - The end position of the phenotype "pheno_strand" - The strand orientation of the phenotype "num_var" - The total number of variants tested in cis "distance" - The distance between the phenotype and the tested variant (accounting for strand orientation) "snp_id" - The ID of the tested variant "snp_chr" - The chromosome ID of the variant "snp_start" - The start position of the variant "snp_end" - The end position of the variant "nominal_pval" - The nominal P-value of association between the variant and the phenotype "slope" - The corresponding regression slope "lead_snp" - A binary flag equal to 1 is the variant is the top variant in cis <strong>Permuted eQTL</strong> results include only the top SNP-gene association for each gene (1000 permutations). Table columns are formatted as follows: "gene_id" - The phenotype ID "gene_chr" - The chromosome ID of the phenotype "gene_start" - The start position of the phenotype "gene_end" - The end position of the phenotype "gene_strand" - The strand orientation of the phenotype "num_var" - The total number of variants tested in cis "distance" - The distance between the phenotype and the tested variant (accounting for strand orientation) "snp_id" - The ID of the top variant "snp_chr" - The chromosome ID of the top variant "snp_start" - The start position of the top variant "snp_end" - The end position of the top variant "degree_of_freedom" - The number of degrees of freedom used to compute the P-values "dummy" - Dummy "bval1" - The first parameter value of the fitted beta distribution "bval2" - The second parameter value of the fitted beta distribution (it also gives the effective number of independent tests in the region) "nominal_pval" - The nominal P-value of association between the phenotype and the top variant in cis "slope" - The corresponding regression slope "empirical_pval" - The P-value of association adjusted for the number of variants tested in cis given by the direct method (i.e. empirircal P-value) "beta_dist_pval" - The P-value of association adjusted for the number of variants tested in cis given by the fitted beta distribution. We strongly recommend to use this adjusted P-value in any downstream analysis <strong>Nominal sQTL</strong> results include all SNP-junction pairs tested (using a 100kb window from the center of each intron cluster). Table columns are formatted as follows: "pheno_id" - The phenotype ID "pheno_chr" - The chromosome ID of the phenotype "pheno_start" - The start position of the phenotype "pheno_end" - The end position of the phenotype "pheno_strand" - The strand orientation of the phenotype "num_var" - The total number of variants tested in cis "distance" - The distance between the phenotype and the tested variant (accounting for strand orientation) "snp_id" - The ID of the tested variant "snp_chr" - The chromosome ID of the variant "snp_start" - The start position of the variant "snp_end" - The end position of the variant "nominal_pval" - The nominal P-value of association between the variant and the phenotype "slope" - The corresponding regression slope "lead_snp" - A binary flag equal to 1 is the variant is the top variant in cis <strong>Permuted sQTL</strong> results include only the top SNP-junction association by gene (1000 permutations). Table columns are formatted as follows: "pheno_id" - The phenotype group ID (here a gene ID) "pheno_chr" - The chromosome ID of the phenotype group "pheno_start" - The start position of the phenotype group "pheno_end" - The end position of the phenotype group "pheno_strand" - The strand orientation of the phenotype group "pheno_id" - The top phenotype in the group (here an exon ID) "num_pheno" - The total number of phenotypes in the group (i.e. #exons) "num_var" - The total number of variants tested in cis "distance" - The distance between the phenotype group and the tested variant (accounting for strand orientation) "snp_id" - The ID of the top variant "snp_chr" - The chromosome ID of the top variant "snp_start" - The start position of the top variant "snp_end" - The end position of the top variant "degree_of_freedom” - The number of degrees of freedom used to compute the P-valuesm" "dummy" - Dummy "bval1" - The first parameter value of the fitted beta distribution "bval2" - The second parameter value of the fitted beta distribution (it also gives the effective number of independent tests in the region) "nominal_pval" - The nominal P-value of association between the top phenotype and the top variant in cis "slope" - The corresponding regression slope "empirical_pval" - The P-value of association adjusted for the number of variants and phenotypes tested in cis given by the direct method (i.e. empirircal P-value) "beta_dist_pval" - The P-value of association adjusted for the number of variants and phenotypes tested in cis given by the fitted beta distribution. We strongly recommend to use this adjusted P-value in any downstream analysis <strong>NOTE:</strong> The effect sizes of eQTLs and sQTL are defined as the effect of the alternative allele (ALT) relative to the reference (REF) allele in the human genome reference (GRCh38).