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Table 4 The comparison results of the most impacted pathways and impact direction under decision analysis model, KEGG-PATH and DIA method

From: A decision analysis model for KEGG pathway analysis

 

KEGG pathway Categories/Sub-categories

The concordance rate of impact direction

The concordance rate of the most impacted pathways

Decision analysis

KEGG-PATH

DIA

KEGG-PATH

1

1. Metabolism

For its sub-category pathways

54.5 %(6/11)

45.5 %(5/11)

62.5 % (5/8)

87.5 %(7/8)

2

3. Environmental Information Processing

100 %(3/3)

33.3 %(1/3)

0 (0/1)

100 %(1/1)

3

1.1 Carbohydrate Metabolism

For its secondary pathways

35.7 % (5/14)

50 %(7/14)

40 % (2/5)

50 % (3/6)

4

1.2 Energy Metabolism

33.3 %(1/3)

33.3 %(1/3)

100 %(2/2)

100 %(2/2)

5

1.3 Lipid Metabolism

76.9 %(10/13)

30.8 %(4/13)

50 %(3/6)

33.3 %(2/6)

6

1.4 Nucleotide Metabolism

50 %(1/2)

0 (0/2)

100 %(2/2)

100 %(2/2)

7

1.5 Amino Acid Metabolism

54.5 %(6/11)

72.7 %(8/11)

50 %(2/4)

60 %(3/5)

8

1.6 Metabolism of Other Amino Acids

75 %(3/4)

75 %(3/4)

100 %(2/2)

100 %(2/2)

9

1.7 Glycan Biosynthesis and Metabolism

58.3 %(7/12)

41.7 %(5/12)

50 %(2/4)

25 %(1/4)

10

1.8 Metabolism of Cofactors and Vitamins

37.5 %(3/8)

37.5 %(3/8)

60 %(3/5)

60 %(3/5)

11

1.11 Xenobiotics Biodegradation and Metabolism

66.7 %(2/3)

100 %(3/3)

50 %(1/2)

100 %(2/2)

12

3.2 Signal Transduction

63.6 %(7/11)

63.6 %(7/11)

60 %(3/5)

60 %(3/5)

13

3.3 Signaling Molecules and Interaction

66.7 %(2/3)

33.3 %(1/3)

100 %(3/3)

100 %(3/3)

  1. For the ‘The concordance rate of impact direction’ column, the denominator of each fraction in the parentheses denotes the number of subcategory pathways and the secondary pathways from the front corresponding categories and sub-categories for two columns, and the numerator of each fraction for two columns denotes the number of pathways with the same impact direction under DIA and decision analysis, and under DIA and KEGG-PATH respectively. For the ‘The concordance rate of the most impacted pathways’ column, the denominator of each fraction in the parentheses denotes the number (a) of the most impacted pathways identified based on DC values in corresponding pathway categories and sub-categories for two columns, and the numerator of each fraction for two columns denotes the number of pathways which also appeared in top a pathways identified by DIA average impact values and by total effect from KEGG-PATH, respectively