Extended Data Fig. 5: Comparing prioritization criteria. | Nature Genetics

Extended Data Fig. 5: Comparing prioritization criteria.

From: Leveraging polygenic enrichments of gene features to predict genes underlying complex traits and diseases

Extended Data Fig. 5: Comparing prioritization criteria.The alternative text for this image may have been generated using AI.

Precision-recall plots for each method with varying prioritization criteria. Each point shows the precision and recall for a set of prioritized genes selected using prioritization criteria based on absolute thresholds and/or relative rank in a locus. For all methods, the star represents the final chosen criteria. a, Circles: PoP scores ranked ≤ 2–5 in the locus. Star: highest PoPS score in the locus. b, Plus: significant TWAS P value after Bonferroni correction (P < 0.05/235,584). Circles: TWAS P values ranked ≤ 2–5 in the locus. Star: significant TWAS P value after Bonferroni correction (P < 0.05/235,584) and the most significant in the locus. c, Pluses: CLPP > 0.01, 0.1, 0.5, 0.9, and 0.99. Circles: CLPP > 0.01, 0.1, 0.5, 0.9, and 0.99 and also the highest CLPP in the locus. Star: CLPP > 0.1 and also the highest CLPP in the locus. d, Plus: any predicted connection from ABC. Circles: ABC connection strength ranked ≤ 2–5 in the locus. Star: highest ABC connection strength in the locus. e, Pluses: any predicted connection from PCHiC for individual datasets. Triangle: any predicted connection from PCHi-C in any dataset. Circles: highest connection strength in the locus for individual datasets. Star: highest connection strength in the locus in any dataset. f, Pluses: any predicted connection from E-P correlation for individual datasets. Triangle: any predicted connection from E-P correlation in any dataset. Circles: highest connection strength in the locus for individual datasets. Star: highest connection strength in the locus in any dataset. g, Circle: closest gene by distance to the transcription start site. Star: closest gene by distance to the gene body. h, Circles: MAGMA z-scores ranked ≤ 2–5 in the locus. Star: highest MAGMA score in the locus. i, Plus: significant SMR P value after Bonferroni correction (P < 0.05/18,383). Circles: SMR P values ranked ≤ 2–5 in the locus. Star: significant SMR P value after Bonferroni correction (P < 0.05/18,383) and the most significant in the locus.

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