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Table 1 Top-enriched GO biological process gene sets by NES, based on p value and confect rankings. Columns “Up” and “Down” are the percent significantly upregulated and downregulated genes in the cancer samples at 5% FDR

From: Topconfects: a package for confident effect sizes in differential expression analysis provides a more biologically useful ranked gene list

Ranking method

GO term

Description

NES

Genes

Up (%)

Down (%)

p value

GO:0051301

Cell division

4.81

582

54

30

GO:0000819

Sister chromatid segregation

4.42

232

65

20

GO:0007049

Cell cycle

4.41

1778

48

34

GO:0022402

Cell cycle process

4.35

1309

50

32

GO:0007059

Chromosome segregation

4.34

344

60

23

GO:0098813

Nuclear chromosome segregation

4.18

295

60

23

GO:0000070

Mitotic sister chromatid segregation

4.12

149

62

21

GO:1903047

Mitotic cell cycle process

4.08

826

54

28

GO:0000278

Mitotic cell cycle

3.99

1003

52

30

GO:0006334

Nucleosome assembly

3.86

106

74

18

Confect

GO:0003008

System process

6.32

1472

26

52

GO:0007186

G protein-coupled receptor signaling pathway

5.35

771

29

51

GO:0009888

Tissue development

5.23

1686

36

43

GO:0035295

Tube development

5.16

918

31

47

GO:0007267

Cell-cell signaling

5.11

1481

35

45

GO:0048646

Anatomical structure formation involved in morphogenesis

4.92

971

32

48

GO:0001568

Blood vessel development

4.87

608

29

52

GO:0006928

Movement of cell or subcellular component

4.85

1815

35

44

GO:0040011

Locomotion

4.85

1578

35

45

GO:0010469

Regulation of signaling receptor activity

4.84

413

34

47