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Table 3 Validation and comparison to other methods in a gender benchmark dataset

From: Inferring pathway dysregulation in cancers from multiple types of omic data

C1 cannonical gene sets (MSigDB)

GSOA

GSEA

GAGE

GSAA

 

Rank

P

FDR

Rank

P

FDR

Rank

P

FDR

Rank

P

FDR

chrY

1

0.001

0.079

1

0.000

0.000

1

0.001

0.297

1

0.000

0.105

chrYq11

1

0.001

0.079

1

0.000

0.000

2

0.002

0.335

1

0.000

0.105

chrYp11

1

0.001

0.079

1

0.000

0.002

6

0.052

0.923

1

0.000

0.210

chrXq26

17

0.035

0.623

114

0.652

0.961

316

0.979

0.979

284

0.892

0.959

chrXp22

156

0.505

0.985

4

0.002

1.000

3

0.008

0.895

1

0.000

1

# of sig. gene sets

29

7

6

21

C2 cannonical gene sets (MsigDB)

            

X-inactivation genes

17

0.031

0.770

1

0.000

0.000

2

0.008

0.914

1

0.000

0.135

Testis genes

71

0.127

0.885

1

0.000

0.067

3

0.008

0.914

1

0.000

0.890

GNF female genes

499

0.943

0.982

3

0.010

0.067

1

0.005

0.914

1

0.000

0.520

# of sig. gene sets

34

8

7

23

  1. We used the various methods to compare gene-expression levels between male and female cell lines