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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
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