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Table 5 Gene ontologies regulated by P53 knockdown

From: P53 in human melanoma fails to regulate target genes associated with apoptosis and the cell cycle and may contribute to proliferation

 

Biological Process

% of genes regulated by p53 in Melan. (from 673 unique genes)

Over/under

p-value

% of genes regulated by p53 in IgR3 (from 552 unique genes)

Over/under

p-value

% of genes regulated by p53 in Mel-RM (from 380 unique genes)

Over/under

p-value

1

Mitosis

7.28

+

1.36E-07

4.53

+

5.32E-02

5.00

+

3.80E-02

2

Cellular process

40.86

+

1.55E-07

40.40

+

5.36E-06

41.32

+

3.07E-05

3

Cell cycle

14.71

+

3.28E-06

11.78

+

2.68E-02

11.58

+

7.22E-02

4

Cytokinesis

3.42

+

1.05E-05

1.45

+

3.41E-01

1.05

-

5.23E-01

5

Nucleobase, nucleoside, nucleotide and nucleic acid metabolic process

25.85

+

1.50E-05

19.57

+

4.33E-01

16.05

-

6.48E-02

6

Metabolic process

48.89

+

6.80E-05

47.83

+

1.60E-03

43.68

+

2.10E-01

7

Primary metabolic process

47.25

+

6.93E-05

45.83

+

2.78E-03

41.84

+

2.38E-01

8

Chromosome segregation

2.82

+

1.09E-04

0.91

-

4.93E-01

1.84

+

1.03E-01

9

Vesicle-mediated transport

9.06

+

5.16E-04

9.42

+

5.34E-04

8.95

+

9.33E-03

10

Anatomical structure morphogenesis

8.62

+

1.03E-03

8.70

+

2.18E-03

8.95

+

5.71E-03

11

Cellular component morphogenesis

8.62

+

1.03E-03

8.70

+

2.18E-03

8.95

+

5.71E-03

12

Ectoderm development

10.40

+

1.26E-03

10.14

+

5.92E-03

11.05

+

3.70E-03

13

Localization

1.63

+

1.27E-03

1.81

+

9.74E-04

0.79

+

3.35E-01

14

Nervous system development

9.36

+

1.38E-03

8.33

+

3.56E-02

10.00

+

3.79E-03

15

Cellular component organization

10.40

+

1.70E-03

11.05

+

7.71E-04

10.26

+

1.87E-02

16

Cell-cell signaling

9.66

+

2.12E-03

11.96

+

4.33E-06

7.63

+

2.57E-01

17

Lipid metabolic process

8.32

+

2.56E-03

9.06

+

7.31E-04

7.89

+

4.00E-02

18

Defense response to bacterium

1.19

+

3.85E-03

1.27

+

4.74E-03

0.53

+

4.06E-01

19

System process

14.41

+

5.19E-03

14.86

+

4.42E-03

13.68

+

6.96E-02

20

Meiosis

2.08

+

6.73E-03

1.27

+

2.86E-01

2.11

+

3.29E-02

  1. Analysis of the top 20 biological processes regulated by P53 knockdown (control shRNA versus P53 shRNA) in melanocytes (Melan.) compared to IgR3 and Mel-RM cell lines using the PANTHER database and gene expression analysis tool [26]. The data are represented as the percentage of genes regulated in each category from the entire gene list (> 2-fold change, p ≤ 0.05, FDR = 5.0% in comparisons of control shRNA with P53 shRNA) for each cell line. P-values for biological processes that were significantly over or under represented (+/-) in comparisons of the gene lists between P53-regulated genes (from Melanocytes, IgR3 or Mel-RM) and the human reference list are shown in the table, while biological processes that were significantly different (p < 0.05) between melanocytes and either of the melanoma cell lines are highlighted in bold.