Results for eQTL analysis for each brain region

This dataset is part of the manuscript: "<em>Atlas of genetic effects in human microglia transcriptome across brain regions, aging and disease pathologies</em>", by Lopes KP, Snijders GJL, Humphrey J, et al. Description of files: <em>MFG_eur_expression_peer10.cis_qtl_nominal.txt.gz - </em>Full <strong>nominal eQTL</strong> summary statistics from medial frontal gyrus (<strong>MFG</strong>)<em> </em>(gzip-compressed) <em>STG_eur_expression_peer10.cis_qtl_nominal.txt.gz </em>- Full <strong>nominal eQTL</strong> summary statistics from superior temporal gyrus (<strong>STG</strong>) (gzip-compressed) <em>SVZ_eur_expression_peer5.cis_qtl_nominal.txt.gz - </em>Full <strong>nominal eQTL</strong> summary statistics from subventricular zone (<strong>SVZ</strong>)<em> </em>(gzip-compressed) <em>THA_eur_expression_peer10.cis_qtl_nominal.txt.gz - </em>Full <strong>nominal eQTL</strong> summary statistics from thalamus (<strong>THA</strong>)<em> </em>(gzip-compressed) <em>MFG_eur_expression_peer10.cis_qtl.txt.gz </em>- Full <strong>permuted eQTL</strong> summary statistics from medial frontal gyrus (<strong>MFG</strong>) (gzip-compressed) <em>STG_eur_expression_peer10.cis_qtl.txt.gz -</em> Full <strong>permuted eQTL</strong> summary statistics from superior temporal gyrus (<strong>STG</strong>) (gzip-compressed) <em>SVZ_eur_expression_peer5.cis_qtl.txt.gz - </em>Full <strong>permuted eQTL</strong> summary statistics from subventricular zone (<strong>SVZ</strong>) (gzip-compressed) <em>THA_eur_expression_peer10.cis_qtl.txt.gz - </em>Full <strong>permuted eQTL</strong> summary statistics from thalamus (<strong>THA</strong>) (gzip-compressed) Nominal QTL 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: phenotype_id - ensembl ID of the gene tested (GENCODE v30) variant_id - SNP tested for association (rsid or chr:position:ref:alt) tss_distance - distance of the SNP to the gene transcription start site (TSS) maf - minor allele frequency in MiGA cohort ma_samples - number of samples carrying the minor allele ma_count - total number of minor alleles across individuals pval_nominal - nominal <em>P</em>-value from linear regression slope - slope of the linear regression slope_se - standard error of the slope Permuted QTL results include only the top SNP-gene association for each gene. Table columns are formatted as follows: phenotype_id - ensembl ID of the gene tested (GENCODE v30) num_var - total number of variants tested in <em>cis</em> beta_shape1 - first parameter value of the fitted beta distribution beta_shape2 - second parameter value of the fitted beta distribution true_df - effective degrees of freedom the beta distribution approximation pval_true_df - empirical <em>P</em>-value for the beta distribution approximation variant_id - ID of the top variant (rsid or chr:position:ref:alt) tss_distance - distance of the SNP to the gene transcription start site (TSS) ma_samples - number of samples carrying the minor allele ma_count - total number of minor alleles across individuals maf -minor allele frequency in MiGA cohort ref_factor - flag indicating if the alternative allele is the minor allele in the cohort (1 if AF &lt;= 0.5, -1 if not) pval_nominal - nominal <em>P</em>-value from linear regression slope - slope of the linear regression slope_se - standard error of the slope pval_perm - first permutation <em>P</em>-value directly obtained from the permutations with the direct method pval_beta - second permutation <em>P</em>-value obtained via beta approximation. This is the one to use for downstream analysis qval - Storey q-value derived from pval_beta (FDR adjusted) pval_nominal_threshold - nominal <em>P</em>-value threshold for calling a variant-gene pair significant for the gene <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). A file containing that information for all alleles tested is available at 10.5281/zenodo.4301005本数据集隶属于研究论文：*《人脑小胶质细胞转录组在不同脑区、衰老及疾病病理中的遗传效应图谱》*（Atlas of genetic effects in human microglia transcriptome across brain regions, aging and disease pathologies），作者为Lopes KP、Snijders GJL、Humphrey J等。 ### 文件描述 所有文件均为gzip压缩格式： 1. **MFG_eur_expression_peer10.cis_qtl_nominal.txt.gz**：内侧前额叶皮层（medial frontal gyrus, MFG）的全量标称表达数量性状基因座（expression Quantitative Trait Locus, eQTL）汇总统计量文件 2. **STG_eur_expression_peer10.cis_qtl_nominal.txt.gz**：颞上回（superior temporal gyrus, STG）的全量标称eQTL汇总统计量文件 3. **SVZ_eur_expression_peer5.cis_qtl_nominal.txt.gz**：室管膜下区（subventricular zone, SVZ）的全量标称eQTL汇总统计量文件 4. **THA_eur_expression_peer10.cis_qtl_nominal.txt.gz**：丘脑（thalamus, THA）的全量标称eQTL汇总统计量文件 5. **MFG_eur_expression_peer10.cis_qtl.txt.gz**：内侧前额叶皮层（MFG）的全量置换eQTL汇总统计量文件 6. **STG_eur_expression_peer10.cis_qtl.txt.gz**：颞上回（STG）的全量置换eQTL汇总统计量文件 7. **SVZ_eur_expression_peer5.cis_qtl.txt.gz**：室管膜下区（SVZ）的全量置换eQTL汇总统计量文件 8. **THA_eur_expression_peer10.cis_qtl.txt.gz**：丘脑（THA）的全量置换eQTL汇总统计量文件 ### 标称QTL结果说明 标称QTL结果包含所有检测的SNP-基因对（检测窗口为基因转录起始位点（transcription start site, TSS）上下游各1Mb范围）。表格列格式说明如下： - phenotype_id：所检测基因的Ensembl ID（对应GENCODE v30版本） - variant_id：用于关联分析的SNP，可为rs号或格式为chr:position:ref:alt的位点标识 - tss_distance：该SNP与基因转录起始位点（TSS）的距离 - maf：MiGA队列中的次要等位基因频率 - ma_samples：携带次要等位基因的样本数 - ma_count：所有个体中次要等位基因的总计数 - pval_nominal：线性回归得到的标称P值 - slope：线性回归的斜率（即效应量） - slope_se：斜率的标准误 ### 置换QTL结果说明 置换QTL结果仅包含每个基因的最优SNP-基因关联对。表格列格式说明如下： - phenotype_id：所检测基因的Ensembl ID（对应GENCODE v30版本） - num_var：顺式（cis）区域内检测的总变异数 - beta_shape1：拟合β分布的第一个参数值 - beta_shape2：拟合β分布的第二个参数值 - true_df：β分布近似的有效自由度 - pval_true_df：β分布近似得到的经验P值 - variant_id：最优变异的ID，可为rs号或格式为chr:position:ref:alt的位点标识 - tss_distance：该SNP与基因转录起始位点（TSS）的距离 - ma_samples：携带次要等位基因的样本数 - ma_count：所有个体中次要等位基因的总计数 - maf：MiGA队列中的次要等位基因频率 - ref_factor：标记该群体中替代等位基因是否为次要等位基因：若等位基因频率≤0.5则为1，否则为-1 - pval_nominal：线性回归得到的标称P值 - slope：线性回归的斜率（即效应量） - slope_se：斜率的标准误 - pval_perm：直接置换法得到的首次置换P值 - pval_beta：通过β分布近似得到的二次置换P值，为下游分析推荐使用的指标 - qval：基于pval_beta计算得到的Storey q值（即错误发现率（FDR）校正后的P值） - pval_nominal_threshold：该基因判定变异-基因对为显著关联的标称P值阈值 **注**：eQTL与剪接数量性状基因座（splicing Quantitative Trait Locus, sQTL）的效应量定义为相对于人类基因组参考序列（GRCh38）中参考等位基因（REF）的替代等位基因（ALT）的效应。包含所有检测等位基因相关信息的文件可在10.5281/zenodo.4301005获取。