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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.