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Table 2 Significant pathways identified by Approach 1 (meta-analysis of cohort-specific pathway enrichment effects and tests)

From: Multi-omics and pathway analyses of genome-wide associations implicate regulation and immunity in verbal declarative memory performance

 

Meta discovery

PAR-dr

WL-dr

Gene set (size)

Effect

SE

RE_p

Bin_pA

Effect

SE

RE_p

Bin_pA

 Type 1 diabetes (44)

20.94%

1.22%

3.32E − 66

5.79E − 03

22.67%

1.72%

7.59E − 40

2.32E − 10

 PSMD4 targets (73)

14.33%

1.11%

7.24E − 38

5.79E − 03

15.40%

1.20%

8.44E − 38

1.83E − 07

 Graft-versus-host disease (42)

24.26%

1.69%

1.60E − 46

1.54E − 05

25.60%

2.07%

4.17E − 35

2.32E − 10

 Allograft rejection (38)

25.57%

1.34%

3.98E − 81

4.01E − 07

27.73%

1.99%

3.28E − 44

7.42E − 09

 Antigen processing and presentation (89)

12.53%

0.88%

1.52E − 46

5.79E − 03

13.05%

1.31%

1.70E − 23

3.52E − 06

 Viral myocarditis (73)

11.76%

0.94%

6.97E − 36

 > 0.05

13.51%

1.04%

1.05E − 38

5.28E − 05

 

Meta replication

 

PAR-dr

WL-dr

Gene set

Effect

SE

RE_p

Bin_pǂ

Effect

SE

RE_p

Bin_pǂ

 Type 1 diabetes

0.63%

1.47%

0.67

1.00

3.44%

1.83%

0.060

0.006

 PSMD4 targets

0.39%

1.01%

0.70

1.00

1.88%

0.94%

0.046

0.34

 Graft-versus-host disease

 − 0.48%

1.28%

0.71

1.00

2.64%

1.36%

0.053

0.34

 Allograft rejection

0.28%

1.34%

0.83

1.00

1.42%

1.76%

0.42

0.34

 Antigen processing and presentation

 − 1.25%

0.86%

0.15

1.00

2.19%

1.56%

0.16

0.34

 Viral myocarditis

0.40%

1.13%

0.72

0.34

1.52%

1.44%

0.29

0.057

 

Meta joint

 

PAR-dr

WL-dr

Gene set

Effect

SE

RE_p

Bin_pA

Effect

SE

RE_p

Bin_pA

 Type 1 diabetes

10.78%

2.77%

1.01E − 04

0.04

15.98%

2.32%

6.23E − 12

6.11E − 08

 PSMD4 targets

7.36%

1.94%

1.50E − 04

0.04

10.69%

1.60%

2.70E − 11

9.71E − 06

 Graft-versus-host disease

11.88%

3.35%

3.97E − 04

8.57E − 04

17.60%

2.72%

1.04E − 10

6.11E − 08

 Allograft rejection

12.93%

3.38%

1.33E − 04

8.09E − 05

18.57%

3.02%

7.73E − 10

8.39E − 07

 Antigen processing and presentation

5.64%

1.86%

2.43E − 07

0.04

9.27%

1.48%

3.98E − 10

9.40E − 05

 Viral myocarditis

6.08%

1.61%

1.54E − 04

0.04

9.34%

1.47%

2.05E − 10

7.53E − 04

  1. This table shows the significant pathways identified through the meta-analysis of cohort-specific pathway enrichment effects (random effects model) or tests (binomial tests). Results are shown for the meta-analysis of discovery cohorts alone, replication cohorts alone, and the discovery and replication cohorts combined. Gene set (Size) is the name of the gene set and the number of genes it included. Effect indicates the increased probability of a pathway component gene to have a significant measure of association (U-score ≤ 0.05) compared to a random gene. SE is the standard error of the effect; PAR-dr and WL-dr are the meta-analysis results for the paragraph and word list delayed recall assessments, respectively. RE_p is the p-value from the meta-analysis using the random effects model. Bin_pA is the meta-analysis permutation-adjusted p-value from the binomial test. Bin_p is the meta-analysis exact p-value from the binomial test that does not adjust for multiple testing. ǂOnly six pathways were tested for replication, thus the exact path p-values (Bin_p) were used instead of the permutation-adjusted adjusted p-values (Bin_pA) when meta-analyzing pathway results across cohorts
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Alzheimer's Research & Therapy

ISSN: 1758-9193