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3 results for “colocalization analysis”
Results for eQTL and sQTL meta-analysis and colocalization
<p>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.</p> <p> </p> <p>Description of files:</p> <p><em>COLOC_supp_table_all_results.tsv.gz - </em>Table with results from <strong>COLOC</strong><em> </em>(gzip-compressed). Table columns are formatted as follows:</p> <ol> <li>disease - disease name (Alzheimer’s disease - AD, Bipolar Disorder - BPD, Multiple sclerosis - MS, Parkinson’s disease - PD, Schizohphrenia - SCZ)</li> <li>GWAS - GWAS study (IMSGC_2019, Jansen_2018, Kunkle_2019, Lambert_2013, Marioni_2018, Nalls23andMe_2019, Ripke_2014, Stahl_2019)</li> <li>locus - locus id according to each GWAS study</li> <li>GWAS_SNP - SNP reported in the GWAS study</li> <li>GWAS_P - <em>P</em>-value of the GWAS_SNP reported in the GWAS study</li> <li>GWAS_chr - chromosome of the GWAS_SNP (hg38)</li> <li>GWAS_pos - genomic position in the chromosome of the GWAS_SNP (hg38)</li> <li>QTL - id for the QTL study</li> <li>type - the type of QTL (eQTL or sQTL)</li> <li>QTL_SNP - SNP id from the QTL association</li> <li>QTL_P - <em>P</em>-value for the QTL association </li> <li>QTL_Beta - Slope (beta) for the QTL association</li> <li>QTL_MAF - minor allele frequency for the QTL_SNP in each QTL study. If not available, values were obtained from the European superpopulation of 1000 Genomes phase 3</li> <li>QTL_chr - chromosome for the QTL_SNP (hg38)</li> <li>QTL_pos - genomic position in the chromosome of the QTL_SNP (hg38)</li> <li>QTL_junction - splicing junction tested in the association (for sQTLs only)</li> <li>QTL_Gene - gene name for the QTL association</li> <li>QTL_Ensembl - Ensembl gene id for the QTL_gene (GENCODE v30)</li> <li>nsnps - number of SNPs tested </li> <li>PP.H0.abf - posterior probability for H0 (no causal variant)</li> <li>PP.H1.abf - posterior probability for H1 (causal variant for trait 1 only)</li> <li>PP.H2.abf - posterior probability for H2 (causal variant for trait 2 only)</li> <li>PP.H3.abf - posterior probability for H3 (two distinct causal variants)</li> <li>PP.H4.abf - posterior probability for H4 (one common causal variant)</li> <li>cell_type - cell type of the QTL study</li> <li>SNP_distance - the absolute distance between GWAS_SNP and QTL_SNP</li> <li>LD - linkage disequilibrium between the GWAS_SNP and the QTL_SNP according to 1000 genomes phase 3 European reference panel 3 (only for PP4>0.5, -Inf otherwise)</li> </ol> <p><em>mashR_lfsr_eQTL.txt.gz - </em><strong>mashR </strong>results for <strong>eQTL</strong><em> </em>(gzip-compressed). Table columns are formatted as follows:</p> <ol> <li>ensembl_snp - Ensembl ID and the SNP prioritized by mashR (best SNP per gene)</li> <li>MFG_eur_expression_peer10.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the MFG region</li> <li>STG_eur_expression_peer10.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the STG region</li> <li>SVZ_eur_expression_peer5.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the SVZ region</li> <li>THA_eur_expression_peer10.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the THA region</li> </ol> <p><em>mashR_lfsr_eQTL.txt.gz - </em><strong>mashR </strong>results for <strong>sQTL</strong><em> </em>(gzip-compressed). Table columns are formatted as follows:</p> <ol> <li>pos_ensembl_rsnp - splicing junction coordinates, Ensembl ID, and SNP ID prioritized by mashR (best SNP per junction)</li> <li>MFG_eur_rsplicing_peer5_gene.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the MFG region</li> <li>STG_eur_rsplicing_peer5_gene.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the STG region</li> <li>SVZ_eur_rsplicing_peer0_gene.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the SVZ region</li> <li>THA_eur_rsplicing_peer5_gene.cis_qtl_nominal - local false sign rate (lfsr) of the gene-SNP pair for the THA region</li> </ol> <p><em>out_mfg_stg_svz_tha.metasoft.gz - </em><strong>METASOFT</strong> results<strong> </strong>for <strong>eQTLs</strong> meta-analysis from MiGA four brain regions<em> </em>(gzip-compressed). Table columns are formatted as follows:</p> <ol> <li>RSID - Id composed by gene Ensembl and SNP ID separated by an underscore for each gene-SNP pair tested in the eQTL study</li> <li>#STUDY - number of studies included in the meta-analysis</li> <li>PVALUE_FE - <em>P</em>-value of the fixed-effects model (FE) according to METASOFT</li> <li>BETA_FE - Estimated Beta under the fixed-effects model according to METASOFT</li> <li>STD_FE - Standard error of BETA_FE</li> <li>PVALUE_RE - <em>P</em>-value of the random effects model (RE) according to METASOFT</li> <li>BETA_RE - Estimated Beta under the random-effects model (RE) according to METASOFT</li> <li>STD_RE - Standard error of BETA_RE</li> <li>PVALUE_RE2 - <em>P</em>-value of the Han and Eskin's Random Effects model (RE2) according to METASOFT</li> <li>STAT1_RE2 - RE2 statistic mean effect part</li> <li>STAT2_RE2 - RE2 statistic heterogeneity part</li> <li>PVALUE_BE - BE P-value (“NA” in all row, -binary_effects option is not used)</li> <li>I_SQUARE - I-square heterogeneity statistic</li> <li>Q - Cochran's Q statistic</li> <li>PVALUE_Q - Cochran's Q statistic's <em>P</em>-value</li> <li>TAU_SQUARE - Tau-square heterogeneity estimator of DerSimonian-Laird</li> <li>PVALUES_OF_STUDIES(Tab_delimitered) - <em>P</em>-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA</li> <li>MVALUES_OF_STUDIES(Tab_delimitered) - M-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA</li> </ol> <p><em>out_miga_young_mynd_fairfax.metasoft.gz - </em><strong>METASOFT</strong> results<strong> </strong>for <strong>eQTL</strong> meta-analysis from MiGA four brain regions plus microglia eQTL from Young et al. (2019), and monocytes eQTL from Navarro et al. (2020) and Fairfax et al. (2014)<em> </em>(gzip-compressed). Table columns are formatted as follows:</p> <ol> <li>RSID - Id composed by gene Ensembl and SNP ID separated by an underscore for each gene-SNP pair tested in the eQTL study</li> <li>#STUDY - number of studies included in the meta-analysis</li> <li>PVALUE_FE - <em>P</em>-value of the fixed-effects model (FE) according to METASOFT</li> <li>BETA_FE - Estimated Beta under the fixed-effects model according to METASOFT</li> <li>STD_FE - Standard error of BETA_FE</li> <li>PVALUE_RE - <em>P</em>-value of the random effects model (RE) according to METASOFT</li> <li>BETA_RE - Estimated Beta under the random-effects model (RE) according to METASOFT</li> <li>STD_RE - Standard error of BETA_RE</li> <li>PVALUE_RE2 - <em>P</em>-value of the Han and Eskin's Random Effects model (RE2) according to METASOFT</li> <li>STAT1_RE2 - RE2 statistic mean effect part</li> <li>STAT2_RE2 - RE2 statistic heterogeneity part</li> <li>PVALUE_BE - BE P-value (“NA” in all row, -binary_effects option is not used)</li> <li>I_SQUARE - I-square heterogeneity statistic</li> <li>Q - Cochran's Q statistic</li> <li>PVALUE_Q - Cochran's Q statistic's <em>P</em>-value</li> <li>TAU_SQUARE - Tau-square heterogeneity estimator of DerSimonian-Laird</li> <li>PVALUES_OF_STUDIES(Tab_delimitered) - <em>P</em>-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA, 5-Young et al., 6-Navarro et al., 7-Fairfax et al.</li> <li>MVALUES_OF_STUDIES(Tab_delimitered) - M-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA, 5-Young et al., 6-Navarro et al., 7-Fairfax et al.</li> </ol> <p><em>out_mfg_stg_svz_tha_sClusters.metasoft.gz - </em><strong>METASOFT</strong> results<strong> </strong>for <strong>sQTLs</strong> meta-analysis from MiGA four brain regions (gzip-compressed). Table columns are formatted as follows:</p> <ol> <li>RSID - Id composed by splicing junction coordinates, gene Ensembl ID, and SNP ID separated by underscores for each junction-SNP pair tested in the sQTL study (e.g. chr1_962047_962355_ENSG00000187961.14_1:11008:C:G)</li> <li>#STUDY - number of studies included in the meta-analysis</li> <li>PVALUE_FE - <em>P</em>-value of the fixed-effects model (FE) according to METASOFT</li> <li>BETA_FE - Estimated Beta under the fixed-effects model according to METASOFT</li> <li>STD_FE - Standard error of BETA_FE</li> <li>PVALUE_RE - <em>P</em>-value of the random effects model (RE) according to METASOFT</li> <li>BETA_RE - Estimated Beta under the random-effects model (RE) according to METASOFT</li> <li>STD_RE - Standard error of BETA_RE</li> <li>PVALUE_RE2 - <em>P</em>-value of the Han and Eskin's Random Effects model (RE2) according to METASOFT</li> <li>STAT1_RE2 - RE2 statistic mean effect part</li> <li>STAT2_RE2 - RE2 statistic heterogeneity part</li> <li>PVALUE_BE - BE P-value (“NA” in all row, -binary_effects option is not used)</li> <li>I_SQUARE - I-square heterogeneity statistic</li> <li>Q - Cochran's Q statistic</li> <li>PVALUE_Q - Cochran's Q statistic's <em>P</em>-value</li> <li>TAU_SQUARE - Tau-square heterogeneity estimator of DerSimonian-Laird</li> <li>PVALUES_OF_STUDIES(Tab_delimitered) - <em>P</em>-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA</li> <li>MVALUES_OF_STUDIES(Tab_delimitered) - M-values of each study in the respective order 1-MFG, 2-STG, 3-SVZ, 4-THA</li> </ol> <p><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</p>
Bayesian machine learning analysis of single-molecule fluorescence colocalization images
<p>Data files for the "Bayesian machine learning analysis of single-molecule fluorescence colocalization images" manuscript.</p>
Extended data: Impact of admixture and ancestry on eQTL analysis and GWAS colocalization in GTEx
<p>eQTL summary statistics and GWAS colocalization posterior probabilities from eQTL calling in an admixed subcohort of GTEx v8 with local and global ancestry adjustments. For the original, non-peer-reviewed preprint, see <a href="https://www.biorxiv.org/content/10.1101/836825v1">https://www.biorxiv.org/content/10.1101/836825v1</a>. </p> <p>For the related source code, see <a href="https://doi.org/10.5281/zenodo.3924788">https://doi.org/10.5281/zenodo.3924788</a> or <a href="https://github.com/nicolerg/gtex-admixture-la">https://github.com/nicolerg/gtex-admixture-la</a>. </p>
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