Table 5.
Gene ontologies regulated by P53 knockdown
| 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 |
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.