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Table 2 The top 5 pathways identified by each method from APOE genotype to AD in ROSMAP study

From: MCC-SP: a powerful integration method for identification of causal pathways from genetic variants to complex disease

Method Order
1 2 3 4 5
Pearson-SP Path1
(152.8)
Path2
(69.90)
Path3
(69.01)
Path4
(59.54)
Path5
(32.35)
Spearman-SP Path1
(246.54)
Path2
(154.98)
Path4
(125.08)
Path5
(96.00)
Path3
(66.61)
DC-SP Path1
(57.84)
Path3
(41.32)
Path2
(35.91)
Path4
(31.42)
Path6
(24.32)
MIC-SP Path3
(3063.17)
Path1
(1136.26)
Path6
(1099.96)
Path2
(743.01)
Path4
(380.01)
MI-SP Path3
(60.95)
Path6
(39.72)
Path2
(33.01)
Path5
(25.26)
Path1
(21.32)
MCC-SP Path1
(13.80)
Path3
(12.32)
Path4
(8.87)
Path6
(8.84)
Path2
(7.42)
  1. Note: The pathway importance scores (PISs) were shown in the parenthesis. Note that the PIS is only comparable across one specific method
  2. Path1: APOE genotype →APOE gene expression→GRIN2A → CAPN2 → MAPT→AD
  3. Path2: APOE genotype →APOE gene expression →GRIN2A → MAPK1 → CASP3 → AD
  4. Path3: APOE genotype →APOE gene expression →GRIN2A → NOS1 → AD
  5. Path4: APOE genotype →APOE gene expression →CACNA1C → CAPN2 → MAPT→AD
  6. Path5: APOE genotype →APOE gene expression→CACNA1C → MAPK1 → CASP3 → AD
  7. Path6: APOE genotype →APOE gene expression→CACNA1C → NOS1 → AD