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ColocBoost manuscript resources
Main Figures
Figure 2
Figure 2a. Statistical power and False Discovery Rate (FDR) comparisons.
Figure 2b. Representative simulation examples.
Figure 2c. Variant‐level precision‐recall curves.
Figure 2d. Statistical power and False Discovery Rate (FDR) comparisons.
Figure 2e. Statistical power and False Discovery Rate (FDR) comparisons.
Figure 3
Figure 3a. Colocalization patterns across three different molecular trait modalities (expression, splicing, protein abundance).
Figure 3b. Distribution of the number of 95% CoSs corresponding to the different numbers of colocalized traits per locus.
Figure 3c. UpSet plot summarizing the colocalization patterns across 6 pseudo-bulk brain cell-type eQTL data.
Figure 3d. Cell-type specific colocalization versus fine-mapping eQTL.
Figure 3e. Significantly enriched KEGG pathways.
Figure 3f. Homogeneity in causal effect directions.
Figure 3g. Empirical distribution of the number of 95% CoS versus the size of the CoS.
Figure 3h. Distribution of the number of CoSs per gene.
Figure 3i. Shared cell-types in primary CoS and secondary CoS.
Figure 4
Figure 4a. Variant set -level Excess-of-overlap (EOO) analysis.
Figure 4b. Variant set -level Excess-of-overlap (EOO) analysis in bulk region.
Figure 4c. Variant set -level Excess-of-overlap (EOO) analysis in cell types.
Figure 4d. Microglia-specific eQTL colocalization in FCGR2A.
Figure 4d. Multiple xQTL colocalization in SUOX.
Figure 5
Figure 5abc. Disease heritability analyses of variant-level functional annotations derived from ColocBoost.
Figure 5d. Standardized effect sizes of the MaxVCP-xQTL and an analogous score based on the HyPrColoc method.
Figure 6
Figure 6a. UpSet plot comparison.
Figure 6b. Scatter plot across variants in terms of the magnitude of quantile-matched z-scores.
Figure 6c. Distribution of distances from the gene TSS for CoS.
Figure 6d. Precision-recall analysis compared with ENCODE-rE2G links.
Figure 6e. UpSet plot for AD-xQTL colocalization.
Figure 6f. Manhattan plot of variant level MaxVCP from ColocBoost.
Figure 6g. Microglia-specific eQTL colocalization in BLNK.
Figure 6h. Colocalization across multiple xQTLs in CTSH.
Simulation Studies
Phenotype data simulation
Run Colocboost
Other colocalization methods
Colocalization result summary
Secondary simulations
GWAS / weaker signal simulation and ColocBoost
Correlated phenotypes simulation
Null simulation
Fineboost (single trait ColocBoost)
OPERA running
OPERA: simulation using original proportion configuration
Data Application
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Figure 3
Figure 3
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Analysis and results for Figure 3.