Table 2.
Overrepresented gene sets in the upregulated and downregulated expression time-series clusters. Genes are categorized in sets according to their Gene Ontology. Column “Observed” is the number of genes from each category or set assigned to the cluster. ”Expected” is the number of genes that was calculated in the permutation simulation based on the total size of each category and the uniqueness of the profile. The results are order according to the Fold change. Only significant results are shown (Bonferroni corrected p-value < 0.05)
| GO enrichment for Cluster 1 upregulated (Profiles 41 and 42) | |||||
|---|---|---|---|---|---|
| Category ID | Category Name | Observed | Expected | Fold | Corrected p-value |
| GO:0006270 | DNA replication initiation | 5 | 0.1 | 35.5 | <0.001 |
| GO:0044815 | DNA packaging complex | 13 | 0.5 | 27.5 | <0.001 |
| GO:0000786 | nucleosome | 11 | 0.4 | 26 | <0.001 |
| GO:1990104 | DNA bending complex | 11 | 0.4 | 26 | <0.001 |
| GO:0034728 | nucleosome organization | 11 | 0.5 | 22 | <0.001 |
| GO:0006334 | nucleosome assembly | 11 | 0.5 | 22 | <0.001 |
| GO:0065004 | protein-DNA complex assembly | 12 | 0.6 | 20.8 | <0.001 |
| GO:0071824 | protein-DNA complex subunit organization | 12 | 0.6 | 20.8 | <0.001 |
| GO:0031497 | chromatin assembly | 12 | 0.6 | 20.8 | <0.001 |
| GO:0032993 | protein-DNA complex | 18 | 0.9 | 19.3 | <0.001 |
| GO:0006333 | chromatin assembly or disassembly | 12 | 0.6 | 18.8 | <0.001 |
| GO:0006323 | DNA packaging | 14 | 0.8 | 18.2 | <0.001 |
| GO:0006261 | DNA-dependent DNA replication | 7 | 0.4 | 17.1 | <0.001 |
| GO:0000785 | chromatin | 11 | 0.7 | 16.2 | <0.001 |
| GO:0044427 | chromosomal part | 22 | 1.6 | 13.8 | <0.001 |
| GO:0071103 | DNA conformation change | 16 | 1.2 | 13.6 | <0.001 |
| GO:0000079 | regulation of cyclin-dependent protein serine/threonine kinase activity | 5 | 0.4 | 11.5 | 0.022 |
| GO:0071900 | regulation of protein serine/threonine kinase activity | 5 | 0.5 | 10.9 | 0.03 |
| GO:0046982 | protein heterodimerization activity | 9 | 0.8 | 10.8 | <0.001 |
| GO:0019901 | protein kinase binding | 5 | 0.5 | 10 | 0.038 |
| GO:0019900 | kinase binding | 5 | 0.5 | 10 | 0.038 |
| GO:0043549 | regulation of kinase activity | 5 | 0.5 | 9.3 | 0.05 |
| GO:0045859 | regulation of protein kinase activity | 5 | 0.5 | 9.3 | 0.05 |
| GO:0005694 | chromosome | 24 | 2.7 | 9 | <0.001 |
| GO:0051726 | regulation of cell cycle | 10 | 1.1 | 9 | <0.001 |
| GO:0008017 | microtubule binding | 6 | 0.8 | 7.6 | 0.042 |
| GO:0034622 | cellular macromolecular complex assembly | 16 | 2.4 | 6.7 | <0.001 |
| GO:0006461 | protein complex assembly | 15 | 2.4 | 6.3 | <0.001 |
| GO:0070271 | protein complex biogenesis | 15 | 2.4 | 6.3 | <0.001 |
| GO:1903047 | mitotic cell cycle process | 7 | 1.1 | 6.2 | 0.042 |
| GO:0006325 | chromatin organization | 18 | 3 | 6.1 | <0.001 |
| GO:0065003 | macromolecular complex assembly | 16 | 2.6 | 6 | <0.001 |
| GO:0007049 | cell cycle | 21 | 3.8 | 5.5 | <0.001 |
| GO:0051276 | chromosome organization | 21 | 3.8 | 5.5 | <0.001 |
| GO:0071822 | protein complex subunit organization | 15 | 2.9 | 5.3 | <0.001 |
| GO:0043933 | macromolecular complex subunit organization | 16 | 3.1 | 5.1 | <0.001 |
| GO:0022402 | cell cycle process | 14 | 2.8 | 5 | <0.001 |
| GO:0006281 | DNA repair | 13 | 2.6 | 4.9 | <0.001 |
| GO:0022607 | cellular component assembly | 17 | 3.5 | 4.8 | <0.001 |
| GO:0005874 | microtubule | 9 | 2 | 4.5 | 0.048 |
| GO:0006974 | cellular response to DNA damage stimulus | 13 | 2.9 | 4.4 | <0.001 |
| GO:0051301 | cell division | 11 | 2.6 | 4.2 | 0.022 |
| GO:0006260 | DNA replication | 22 | 5.8 | 3.8 | <0.001 |
| GO:0044085 | cellular component biogenesis | 19 | 5.8 | 3.3 | <0.001 |
| GO:0006259 | DNA metabolic process | 47 | 15.3 | 3.1 | <0.001 |
| GO:0006996 | organelle organization | 27 | 9.3 | 2.9 | <0.001 |
| GO:0043228 | non-membrane-bounded organelle | 41 | 14.4 | 2.8 | <0.001 |
| GO:0043232 | intracellular non-membrane-bounded organelle | 41 | 14.4 | 2.8 | <0.001 |
| GO:0043234 | protein complex | 43 | 16.5 | 2.6 | <0.001 |
| GO:0003677 | DNA binding | 44 | 18.6 | 2.4 | <0.001 |
| GO:0016043 | cellular component organization | 34 | 14.5 | 2.3 | <0.001 |
| GO:0071840 | cellular component organization or biogenesis | 35 | 16.3 | 2.2 | 0.006 |
| GO:0032991 | macromolecular complex | 46 | 22.7 | 2 | <0.001 |
| GO:0005634 | nucleus | 71 | 40.3 | 1.8 | <0.001 |
| GO:0005488 | binding | 138 | 101.6 | 1.4 | 0.016 |
| GO:0044699 | single-organism process | 107 | 76.2 | 1.4 | 0.044 |
| GO enrichment for Cluster 0 downregulated (Profiles 0 and 4) | |||||
| Category ID | Category Name | Observed | Expected | Fold | Corrected p-value |
| GO:0006278 | RNA-dependent DNA replication | 20 | 5.5 | 3.7 | 0.002 |
| GO:0003964 | RNA-directed DNA polymerase activity | 15 | 4.4 | 3.4 | 0.03 |
| GO:0015074 | DNA integration | 24 | 9.4 | 2.5 | 0.028 |