Table 1.
Gene set enrichment analysis based on the Reactome database (top 50 based on p-value).
| Pathway Name | p-Value | NES | Size |
|---|---|---|---|
| Gene expression (Transcription) | 3.42 × 10−19 | 1.909039 | 916 |
| Metabolism of RNA | 3.14 × 10−18 | 2.090669 | 526 |
| RNA Polymerase II Transcription | 2.50 × 10−17 | 1.883699 | 820 |
| Processing of Capped Intron-Containing Pre-mRNA | 3.31 × 10−13 | 2.227814 | 223 |
| Cell Cycle | 4.68 × 10−12 | 1.87915 | 503 |
| Generic Transcription Pathway | 1.19 × 10−11 | 1.750073 | 705 |
| mRNA Splicing | 4.21 × 10−11 | 2.190093 | 174 |
| pre-mRNA splicing | 1.59 × 10−10 | 2.178913 | 168 |
| Cell Cycle, Mitotic | 3.26 × 10−10 | 1.870694 | 423 |
| Cell Cycle Checkpoints | 1.22 × 10−7 | 1.903855 | 230 |
| M Phase | 2.68 × 10−7 | 1.754935 | 315 |
| S Phase | 5.32 × 10−7 | 1.958874 | 131 |
| G1/S Transition | 1.52 × 10−6 | 2.018423 | 99 |
| Extracellular matrix organization | 4.83 × 10−6 | −2.067058 | 185 |
| Respiratory electron transport | 6.76 × 10−6 | −2.37502 | 85 |
| Mitotic G1 phase and G1/S transition | 6.94 × 10−6 | 1.900258 | 121 |
| Metabolism | 1.24 × 10−5 | −1.39958 | 1391 |
| Mitotic Metaphase and Anaphase | 1.68 × 10−5 | 1.707057 | 199 |
| Mitotic Anaphase | 1.95 × 10−5 | 1.701565 | 198 |
| DNA Replication | 2.58 × 10−5 | 1.851959 | 114 |
| Transport of Mature mRNA derived from an Intron-Containing Transcript | 2.91 × 10−5 | 1.982446 | 67 |
| DNA Repair | 5.03 × 10−5 | 1.643199 | 240 |
| Synthesis of DNA | 6.43 × 10−5 | 1.816823 | 106 |
| SUMOylation | 6.54 × 10−5 | 1.731646 | 138 |
| Transport of Mature Transcript to Cytoplasm | 7.11 × 10−5 | 1.927207 | 75 |
| DNA Replication Pre-Initiation | 8.43 × 10−5 | 1.856579 | 77 |
| G1/S DNA Damage Checkpoints | 8.51 × 10−5 | 1.900279 | 63 |
| G2/M Checkpoints | 8.74 × 10−5 | 1.780989 | 121 |
| Complex I biogenesis | 9.29 × 10−5 | −2.392202 | 52 |
| RNA Polymerase II Transcription Termination | 9.81 × 10−5 | 1.912934 | 60 |
| Separation of Sister Chromatids | 0.000126 | 1.702185 | 152 |
| SUMO E3 ligases SUMOylate target proteins | 0.000133 | 1.716686 | 133 |
| Mitotic Prometaphase | 0.000142 | 1.679872 | 163 |
| Epigenetic regulation of gene expression | 0.000157 | 1.997729 | 47 |
| RNA Polymerase II Pre-transcription Events | 0.00021 | 1.855255 | 75 |
| The citric acid (TCA) cycle and respiratory electron transport | 0.000253 | −1.974008 | 156 |
| Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. | 0.000285 | −2.125326 | 109 |
| p53-Dependent G1 DNA Damage Response | 0.000305 | 1.921084 | 61 |
| p53-Dependent G1/S DNA damage checkpoint | 0.000305 | 1.921084 | 61 |
| Syndecan interactions | 0.000318 | −2.137732 | 14 |
| Chondroitin sulfate biosynthesis | 0.00032 | −2.018888 | 18 |
| ECM proteoglycans | 0.000339 | −1.985636 | 22 |
| mRNA 3′-end processing | 0.00035 | 1.874325 | 51 |
| Transcriptional Regulation by TP53 | 0.000365 | 1.513781 | 268 |
| DNA Double-Strand Break Repair | 0.000366 | 1.682974 | 114 |
| TP53 Regulates Transcription of Cell Cycle Genes | 0.00044 | 1.955699 | 29 |
| Non-integrin membrane-ECM interactions | 0.000441 | −1.994996 | 18 |
| Cross-presentation of soluble exogenous antigens (endosomes) | 0.000448 | 1.858045 | 41 |
| MET activates PTK2 signaling | 0.000453 | −2.076443 | 14 |
| Cellular responses to external stimuli | 0.000508 | 1.458568 | 323 |
NES = normalized enrichment score; SUMO = small ubiquitin-related modifier protein; ECM = extracellular matrix; MET = mesenchymal–epithelial transition factor; PTK = protein tyrosine kinase.