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Table 1 Gene set enrichment analysis (GSEA) for clusters generated by FCM with the optimal fuzziness value.

From: Network motif-based identification of transcription factor-target gene relationships by integrating multi-source biological data

Cluster ID

# of genes in cluster

Enriched Functional Category

Total Genes in the category

Clustered Genes

P value

1

10

nucleosome

10

9

1.8E-27

  

DNA binding

229

9

7.2E-13

2

25

steroid metabolic process

43

5

4.9E-07

  

steroid biosynthetic process

32

4

5.8E-06

3

5

cytokinesis, completion of separation

11

5

4.9E-15

  

cell separation during cytokinesis

13

5

1.4E-14

4

33

kinetochore

54

5

6.6E-06

  

mitotic cell cycle

271

8

0.000047

5

16

cellular bud

150

6

9.2E-07

  

cytoskeletal part

180

6

2.7E-06

6

29

dolichyl-phosphate-mannose-protein mannosyltransferase activity

7

3

2.8E-06

  

protein amino acid O-linked glycosylation

16

3

0.000043

7

28

transporter activity

338

8

0.000063

  

primary active transmembrane transporter activity

53

4

0.000071

8

37

microtubule

35

4

0.000042

  

cytoplasmic microtubule

14

3

0.00006

9

11

cellular bud neck

115

5

6.9E-07

  

site of polarized growth

152

5

2.7E-06

10

44

N/A

N/A

N/A

N/A

11

37

DNA helicase activity

75

14

1.1E-18

  

mitotic recombination

41

7

2.1E-09

12

16

ribonucleoside-diphosphate reductase activity

4

2

0.000034

  

cell cycle process

440

7

0.000043

13

28

plasma membrane

261

9

8.6E-07

  

transmembrane transporter activity

246

7

0.000063

14

31

leading strand elongation

14

3

0.000035

  

DNA replication

131

8

9.1E-08

  

DNA metabolic process

710

15

1.1E-07

16

22

L-serine ammonia-lyase activity

3

2

0.000033

17

32

microtubule-based process

101

12

1.9E-14

  

microtubule cytoskeleton

94

11

3.3E-13

18

15

N/A

N/A

N/A

N/A

19

20

cellular bud

150

6

4.1E-06

  

site of polarized growth

152

5

0.000078

20

10

cell wall

114

7

5E-11

  

glucanosyltransferase activity

6

2

0.000032

21

6

N/A

N/A

N/A

N/A

22

28

N/A

N/A

N/A

N/A

23

29

pentose transmembrane transporter activity

4

3

3.2E-07

  

fructose transmembrane transporter activity

15

3

0.000035

24

35

chromosome

231

12

1.3E-09

  

mitotic sister chromatid cohesion

22

5

8.4E-08

  

DNA replication

131

8

3.4E-07

25

30

N/A

N/A

N/A

N/A

26

5

N/A

N/A

N/A

N/A

27

8

response to pheromone

94

7

8.6E-13

  

conjugation with cellular fusion

119

7

4.7E-12

28

24

amine transmembrane transporter activity

16

4

2.6E-07

  

polyamine transmembrane transporter activity

10

3

5.3E-06

29

17

sulfur metabolic process

67

11

7.3E-19

  

methionine metabolic process

24

7

7E-14

30

30

cytoskeletal part

180

9

7E-08

  

spindle

80

6

1.4E-06

31

14

energy reserve metabolic process

36

3

0.000055

  

cellular carbohydrate metabolic process

213

5

0.000058

32

15

MCM complex

6

5

1.9E-13

  

pre-replicative complex

15

6

2.4E-13

  

DNA replication preinitiation complex

21

6

2.6E-12

33

6

cell wall

114

5

9.2E-09

  

structural constituent of cell wall

19

3

4.3E-07

34

22

DNA-dependent DNA replication

97

10

5.8E-14

  

replisome

15

5

4.8E-10

  1. To evaluate whether the gene clusters are enriched in some known biological function or process, we performed GSEA for gene clusters generated from FCM clustering with m = 1.1573 and c = 34. The cut off P-value is 0.0001. The enriched function(s) are listed in the table. Significant function(s) are correlated with all gene clusters except cluster 10, 18, 21, 21, 25 and 26.