Extended Data Fig. 4: Comparison of significant protein concordance across orthogonal platforms and external datasets. | Nature Medicine

Extended Data Fig. 4: Comparison of significant protein concordance across orthogonal platforms and external datasets.

From: Shared and disease-specific pathways in frontotemporal dementia and Alzheimer’s and Parkinson’s diseases

Extended Data Fig. 4

a, Of the shared aptamers, we selected the top 15 and bottom 15 significant proteins of selected by GNPC, out of the 30 proteins, 19(63.3%) of them are of the same direction in Alamar, colored by the blue point. b, Same strategy was also applied to the FTD comparison. Due to the sample size limitation, we selected top 5 and bottom 5 significant proteins in GNPC, 8 out of 10 (80%) are of same direction of effect size in Alamar, colored by pink. c, Comparison with the work by Yi-Han et al.: Their work was conducted on the Olink platform, we analyzed the top 10 and bottom 10 significant shared proteins in GNPC based on FDR values. It demonstrated concordance rates of 55% in Discovery (UK Biobank). d, Comparison with the work by Rutledge et al. (SomaScan Stanford-5x): Among the shared top 10 and bottom 10 proteins in GNPC, a concordance rate of 55% was observed. In summary, these analyses underscore the overlap and consistency of protein directional effects across platforms and diseases, offering valuable insights into the reproducibility and cross-platform validation of our findings.

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