Table 1 Open in new tab Comparative...

No.

Review

Methods tested

Datasets

Database (# of gene sets/pathways)

Types of evaluated methods

[13]

KEGG (116)

Topology- and non-topology-based methods

[2]

KEGG (323) and GO (4631)

ORA and FCS methods

[3]

118

KEGG (232)

Topology-based methods

[14]

KEGG (86)

Topology- and non-topology-based methods

[15]

KEGG (114)

Topology-based methods

[16]

GO gene set collection extracted from MSigDB [17] v6.1 (5917)

Widely used pathway enrichment methods

[18]

MSigDB v5.0 (10,295)

Widely used pathway enrichment methods

[9]

KEGG; 150 pathways for all methods except 130 for PathNet [19] and 186 for CePa [20, 21]

Topology- and non-topology-based methods

[22]

C2 collection from MSigDB v4.0 (4722)

Methods differing based on null hypothesis

[23]

KEGG (259) and Metacore™ (88)

ORA and FCS methods

[24]

KEGG (192)

ORA and FCS methods

[25]

KEGG (189)

ORA and FCS methods

Table 1

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Comparative studies evaluating differences across enrichment methods

No.	Review	Methods tested	Datasets	Database (# of gene sets/pathways)	Types of evaluated methods
1	[13]	7	36	KEGG (116)	Topology- and non-topology-based methods
2	[2]	10	75	KEGG (323) and GO (4631)	ORA and FCS methods
3	[3]	7	118	KEGG (232)	Topology-based methods
4	[14]	6	20	KEGG (86)	Topology- and non-topology-based methods
5	[15]	9	3	KEGG (114)	Topology-based methods
6	[16]	13	6	GO gene set collection extracted from MSigDB [17] v6.1 (5917)	Widely used pathway enrichment methods
7	[18]	8	3	MSigDB v5.0 (10,295)	Widely used pathway enrichment methods
8	[9]	10	86	KEGG; 150 pathways for all methods except 130 for PathNet [19] and 186 for CePa [20, 21]	Topology- and non-topology-based methods
9	[22]	11	1	C2 collection from MSigDB v4.0 (4722)	Methods differing based on null hypothesis
10	[23]	16	42	KEGG (259) and Metacore™ (88)	ORA and FCS methods
11	[24]	5	6	KEGG (192)	ORA and FCS methods
12	[25]	7	38	KEGG (189)	ORA and FCS methods

No.	Review	Methods tested	Datasets	Database (# of gene sets/pathways)	Types of evaluated methods
1	[13]	7	36	KEGG (116)	Topology- and non-topology-based methods
2	[2]	10	75	KEGG (323) and GO (4631)	ORA and FCS methods
3	[3]	7	118	KEGG (232)	Topology-based methods
4	[14]	6	20	KEGG (86)	Topology- and non-topology-based methods
5	[15]	9	3	KEGG (114)	Topology-based methods
6	[16]	13	6	GO gene set collection extracted from MSigDB [17] v6.1 (5917)	Widely used pathway enrichment methods
7	[18]	8	3	MSigDB v5.0 (10,295)	Widely used pathway enrichment methods
8	[9]	10	86	KEGG; 150 pathways for all methods except 130 for PathNet [19] and 186 for CePa [20, 21]	Topology- and non-topology-based methods
9	[22]	11	1	C2 collection from MSigDB v4.0 (4722)	Methods differing based on null hypothesis
10	[23]	16	42	KEGG (259) and Metacore™ (88)	ORA and FCS methods
11	[24]	5	6	KEGG (192)	ORA and FCS methods
12	[25]	7	38	KEGG (189)	ORA and FCS methods

In the third column, we report the number of enrichment methods compared in each study (see Supplementary Tables 2 and 3, available online at https://dbpia.nl.go.kr/bib, for details on the methods tested). Here, we would like to note that we differentiate between methods and tools/web applications based on Geistlinger et al. [2]. In the fourth column, we report the number of datasets each study performed comparisons on, all of which were experimental datasets except in [3, 13, 14, 18, 22], which included both experimental and simulated datasets. Finally, the fifth column reports the pathway databases used in each study while the number of pathways is shown between parentheses.

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