Table 5.
Summary of the biological processes and pathways significantly modulated in the UF respect to F NB-hop patients of the test set.
| Biological Process a | Gene Set Id b | Pathway or Process Description c | Number of Genes d | FDR q-Value e | Type of Regulation f | Ontology g |
|---|---|---|---|---|---|---|
| Response to hypoxia | ||||||
| GO: 0071456 | Cellular response to hypoxia | 19 | 1.00 × 10−3 | UP | GO BP | |
| GO: 0001666 | Response to hypoxia | 26 | 2.00 × 10−2 | UP | GO BP | |
| Telomere Maintenance | ||||||
| HSA-180786 | Extension of Telomeres | 17 | 1.68 × 10−10 | UP | RCTME | |
| HSA-157579 | Telomere Maintenance | 21 | 1.64 × 10−9 | UP | RCTME | |
| HSA-174417 | Telomere C-strand (Lagging Strand) Synthesis | 13 | 5.90 × 10−8 | UP | RCTME | |
| GO: 0000723 | Telomere maintenance | 22 | 1.00 × 10−6 | UP | GO BP | |
| GO: 0032201 | Telomere maintenance via semi-conservative replication | 11 | 2.77 × 10−6 | UP | GO BP | |
| Chromatin remodeling | ||||||
| GO: 0031497 | Chromatin assembly | 31 | 9.97 × 10−9 | UP | GO BP | |
| GO: 0031055 | Chromatin remodeling at centromere | 15 | 2.02 × 10−6 | UP | GO BP | |
| GO: 0006325 | Chromatin organization | 66 | 3.32 × 10−6 | UP | GO BP | |
| GO: 0006338 | Chromatin remodeling | 26 | 5.45 × 10−6 | UP | GO BP | |
| DNA damage response | ||||||
| GO: 0051276 | Chromosome organization | 143 | 3.32 × 10−27 | UP | GO BP | |
| GO: 0007059 | Chromosome segregation | 67 | 5.21 × 10−24 | UP | GO BP | |
| HSA-73886 | Chromosome Maintenance | 32 | 1.86 × 10−14 | UP | RCTME | |
| GO: 0006281 | DNA repair | 77 | 4.27 × 10−16 | UP | GO BP | |
| HSA-73894 | DNA Repair | 47 | 9.85 × 10−11 | UP | RCTME | |
| GO: 0006302 | Double-strand break repair | 29 | 1.88 × 10−6 | UP | GO BP | |
| hsa03410 | Base excision repair | 10 | 4.00 × 10−4 | UP | KEGG | |
| GO: 0006284 | Base-excision repair | 9 | 5.00 × 10−3 | UP | GO BP | |
| hsa03430 | Mismatch repair | 6 | 2.00 × 10−2 | UP | KEGG | |
| P53 mediated Cell cycle arrest and cellular senescence | ||||||
| HSA-6791312 | TP53 Regulates Transcription of Cell Cycle Genes | 14 | 6.62 × 10−6 | UP | RCTME | |
| HSA-6804756 | Regulation of TP53 Activity through Phosphorylation | 18 | 1.99 × 10−5 | UP | RCTME | |
| GO:0006977 | DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest | 14 | 1.00 × 10−4 | UP | GO BP | |
| HSA-6804116 | TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest | 7 | 2.40 × 10−4 | UP | RCTME | |
| HSA-6804114 | TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest | 7 | 7.50 × 10−4 | UP | RCTME | |
| hsa04218 | Cellular senescence | 20 | 2.00 × 10−3 | UP | KEGG | |
| hsa04115 | p53 signaling pathway | 12 | 4.00 × 10−3 | UP | KEGG | |
| Cell cycle and proliferation | ||||||
| GO: 0007049 | Cell cycle | 196 | 6.38 × 10−43 | UP | GO BP | |
| GO: 0000278 | Mitotic cell cycle | 136 | 4.17 × 10−42 | UP | KEGG | |
| GO: 0051301 | Cell division | 87 | 1.15 × 10−21 | UP | GO BP | |
| GO: 0008283 | Cell population proliferation | 64 | 1.07 × 10−5 | UP | GO BP | |
| Immune response | ||||||
| GO: 0046649 | Lymphocyte activation | 63 | 1.87 × 10−7 | DOWN | GO BP | |
| GO: 0042110 | T cell activation | 45 | 1.27 × 10−6 | DOWN | GO BP | |
| GO: 0002250 | Immune response | 168 | 7.98 × 10−6 | DOWN | GO BP | |
| Cell differentiation | ||||||
| GO: 0030154 | Cell differentiation | 365 | 2.59× 10−11 | DOWN | GO BP | |
| GO: 0022008 | Neurogenesis | 193 | 6.90 × 10−11 | DOWN | GO BP | |
| GO: 0030182 | Neuron differentiation | 134 | 3.75 × 10−10 | DOWN | GO BP | |
| GO: 0002521 | Leukocyte differentiation | 51 | 2.60 × 10−5 | DOWN | GO BP | |
| GO: 0030217 | T cell differentiation | 29 | 4.39 × 10−5 | DOWN | GO BP | |
| GO: 0030098 | Lymphocyte differentiation | 39 | 1.30 × 10−4 | DOWN | GO BP | |
| Cell motility | ||||||
| GO: 0048870 | Cell motility | 108 | 7.41 × 10−5 | DOWN | GO BP | |
| HSA-1474244 | Extracellular matrix organization | 45 | 1.00 × 10−3 | DOWN | RCTME | |
| GO: 0007155 | Cell adhesion | 141 | 5.55 × 10−15 | DOWN | GO BP | |
| hsa04514 | Cell adhesion molecules (CAMs) | 40 | 3.14 × 10−9 | DOWN | KEGG | |
| Inflammation response | ||||||
| GO: 0006954 | Inflammatory response | 71 | 6.87 × 10−6 | DOWN | GO BP | |
| GO: 0071345 | Cellular response to cytokine stimulus | 111 | 9.18 × 10−5 | DOWN | GO BP | |
| GO: 0050727 | Regulation of inflammatory response | 44 | 6.70 × 10−3 | DOWN | GO BP | |
| hsa04062 | Chemokine signaling pathway | 24 | 2.00 × 10−2 | DOWN | KEGG | |
| Cell death | ||||||
| GO: 0042981 | Regulation of apoptotic process | 153 | 7.90 × 10−4 | DOWN | GO BP | |
| GO: 0043067 | Regulation of programmed cell death | 154 | 0.00086 | DOWN | GO BP | |
| Angiogenesis | ||||||
| GO: 0001568 | Blood vessel development | 61 | 0.00065 | DOWN | GO BP | |
| GO: 0001525 | Angiogenesis | 42 | 2.30 × 10−3 | DOWN | GO BP | |
| GO: 0045766 | Positive regulation of angiogenesis | 25 | 1.20 × 10−2 | DOWN | GO BP | |
a Significant GO biological processes, Reactome terms, and KEGG pathways. GO, Reactome and KEGG enrichment analysis was carried out on genes whose expression in UF NB-hop compared with F NB-hop prediction was significantly modulated. b Official identifier of a GO biological process, Reactome or KEGG pathway. c Official name of a GO biological process, Reactome term or KEGG pathway. d Number of genes of a GO biological process or Reactome term or KEGG pathway whose expression was significantly modulated in UF NB-hop tumors. e FDR q-value estimates the significance of the enrichment of a biological process or a pathway. FDR q-value <= 0.05 are considered acceptable. f Type of regulation of the genes involved in a process or a pathway. g Name of the ontology defining a biological process or pathway. GO BP stands for gene ontology biological process. KEGG stands for Kyoto Encyclopedia of Genes and Genomes. RCTME stands for Reactome.