Table 3 Analysis of gene ontology terms over-represented in 3D cultured cells
From: In vitro three-dimensional modeling of fallopian tube secretory epithelial cells
GO terms over-represented in genes down-regulated in 3D cultured cells | ||||
|---|---|---|---|---|
Term | Exp count | Count | Size | Adjusted P-value |
Organelle fission | 11.106 | 61 | 321 | 2.00E-25 |
Cell division | 8.987 | 50 | 266 | 7.74E-21 |
Mitotic prometaphase | 2.872 | 30 | 83 | 2.50E-20 |
Cell cycle process | 10.267 | 44 | 347 | 7.74E-14 |
Cell cycle checkpoint | 2.962 | 23 | 87 | 3.72E-12 |
Interphase | 11.522 | 41 | 333 | 4.02E-10 |
Chromosome segregation | 2.835 | 20 | 84 | 1.14E-09 |
Regulation of cell cycle process | 8.241 | 33 | 245 | 2.28E-09 |
Cellular component organization or biogenesis | 104.766 | 163 | 3028 | 9.59E-09 |
Cellular component organization at cellular level | 73.542 | 125 | 2225 | 1.97E-08 |
DNA replication | 5.364 | 25 | 157 | 2.37E-08 |
DNA strand elongation involved in DNA replication | 1.073 | 12 | 31 | 3.95E-08 |
Mitotic cell cycle | 5.122 | 24 | 175 | 4.65E-08 |
Negative regulation of cell cycle | 11.162 | 35 | 326 | 2.89E-07 |
DNA metabolic process | 4.759 | 21 | 159 | 1.64E-06 |
Microtubule anchoring | 0.830 | 9 | 24 | 8.20E-06 |
Chromosome organization | 15.877 | 39 | 475 | 2.38E-05 |
Cellular response to stress | 29.513 | 59 | 853 | 2.38E-05 |
Mitosis | 4.269 | 18 | 137 | 3.02E-05 |
Regulation of microtubule-based process | 2.284 | 13 | 66 | 3.94E-05 |
Telomere maintenance via recombination | 0.796 | 8 | 23 | 6.95E-05 |
DNA recombination | 3.716 | 16 | 111 | 8.96E-05 |
Telomere maintenance via semi-conservative replication | 0.830 | 8 | 24 | 9.23E-05 |
Double-strand break repair via homologous recombination | 1.419 | 10 | 41 | 9.61E-05 |
DNA repair | 6.807 | 22 | 206 | 1.17E-04 |
Mitotic spindle organization | 0.865 | 8 | 25 | 1.17E-04 |
Microtubule-based process | 4.335 | 17 | 132 | 1.28E-04 |
Chromosome localization | 0.657 | 7 | 19 | 1.74E-04 |
Regulation of transcription involved in G1/S phase of mitotic cell cycle | 0.692 | 7 | 20 | 2.50E-04 |
CenH3-containing nucleosome assembly at centromere | 0.727 | 7 | 21 | 3.41E-04 |
DNA replication-independent nucleosome organization | 0.727 | 7 | 21 | 3.41E-04 |
DNA packaging | 2.857 | 13 | 84 | 3.56E-04 |
S phase of mitotic cell cycle | 4.325 | 16 | 125 | 4.55E-04 |
Nucleotide-excision repair, DNA gap filling | 0.623 | 6 | 18 | 0.002 |
ATP-dependent chromatin remodeling | 0.934 | 7 | 27 | 0.002 |
Nucleosome assembly | 2.491 | 11 | 72 | 0.002 |
Microtubule-based movement | 3.460 | 13 | 100 | 0.003 |
G1/S transition of mitotic cell cycle | 4.693 | 15 | 138 | 0.004 |
Anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process | 2.733 | 11 | 79 | 0.005 |
Transcription-coupled nucleotide-excision repair | 1.488 | 8 | 43 | 0.006 |
Mitotic sister chromatid segregation | 0.510 | 5 | 15 | 0.006 |
Establishment of organelle localization | 2.371 | 10 | 69 | 0.007 |
Cellular component assembly | 34.876 | 57 | 1008 | 0.007 |
Positive regulation of cell cycle cytokinesis | 0.311 | 4 | 9 | 0.009 |
Mitotic metaphase | 0.138 | 3 | 4 | 0.009 |
Spindle organization | 0.605 | 5 | 18 | 0.013 |
Mitochondrial translation | 0.346 | 4 | 10 | 0.013 |
DNA-dependent DNA replication initiation | 0.934 | 6 | 27 | 0.013 |
G2/M transition DNA damage checkpoint | 0.934 | 6 | 27 | 0.013 |
Maintenance of protein location | 2.630 | 10 | 76 | 0.013 |
G2/M transition of mitotic cell cycle | 3.646 | 12 | 106 | 0.013 |
Phosphatidylinositol-mediated signaling | 2.180 | 9 | 63 | 0.014 |
Maintenance of location in cell | 2.664 | 10 | 77 | 0.014 |
Spliceosomal snRNP assembly | 0.969 | 6 | 28 | 0.015 |
Meiotic cell cycle | 3.737 | 12 | 108 | 0.015 |
Microtubule depolymerization | 0.657 | 5 | 19 | 0.016 |
Telomere organization | 1.799 | 8 | 52 | 0.016 |
Mitotic chromosome condensation | 0.381 | 4 | 11 | 0.016 |
Regulation of attachment of spindle microtubules to kinetochore | 0.173 | 3 | 5 | 0.016 |
Spindle assembly | 1.001 | 6 | 29 | 0.016 |
RNA splicing, via transesterification reactions | 6.747 | 17 | 195 | 0.017 |
Cytoskeleton organization | 12.037 | 25 | 356 | 0.017 |
Macromolecular complex subunit organization | 3.893 | 12 | 119 | 0.020 |
Negative regulation of organelle organization | 4.048 | 12 | 117 | 0.028 |
Attachment of spindle microtubules to kinetochore | 0.205 | 3 | 6 | 0.028 |
Mitotic metaphase plate congression | 0.450 | 4 | 13 | 0.029 |
Response to ionizing radiation | 3.010 | 10 | 87 | 0.030 |
Regulation of cyclin-dependent protein kinase activity | 2.526 | 9 | 73 | 0.032 |
Regulation of mitosis | 1.165 | 6 | 34 | 0.033 |
RNA processing | 20.137 | 35 | 582 | 0.034 |
Metaphase plate congression | 0.069 | 2 | 2 | 0.039 |
Aspartate biosynthetic process | 0.069 | 2 | 2 | 0.039 |
Glutamate catabolic process to aspartate | 0.069 | 2 | 2 | 0.039 |
Glutamate catabolic process to 2-oxoglutarate | 0.069 | 2 | 2 | 0.039 |
Regulation of hippo signaling cascade | 0.069 | 2 | 2 | 0.039 |
Negative regulation of mitotic recombination | 0.069 | 2 | 2 | 0.039 |
Deoxyribonucleotide biosynthetic process | 0.242 | 3 | 7 | 0.040 |
Kinetochore assembly | 0.242 | 3 | 7 | 0.040 |
Protein K6-linked ubiquitination | 0.242 | 3 | 7 | 0.040 |
M phase of mitotic cell cycle | 0.239 | 3 | 8 | 0.041 |
GO terms over-represented in genes upregulated in 3D cultured cells | ||||
Term | Exp count | Count | Size | Adjusted P-value |
Positive regulation of transcription from RNA polymerase II promoter | 9.063 | 26 | 362 | 0.003 |