Table 3

Analysis of gene ontology terms over-represented in 3D cultured 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

80 terms were over-represented in the genes that were underexpressed in 3D and 1 GO term was significantly over-represented in genes upregulated when FTSECs were transitioned to a 3D microenvironment. The majority of these terms were associated with cell cycle progression, mitosis and DNA replication.

Lawrenson et al.

Lawrenson et al. BMC Cell Biology 2013 14:43   doi:10.1186/1471-2121-14-43

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