Table 1.
GO term analysis of the cell cycle dependent transcriptional program of HeLa cells
| GO Term | Gene count | p-value | Bonferroni-corrected p-value | |
|---|---|---|---|---|
| Panel A – genes unique to HeLa SORT experiment | ||||
| GO:0007049 | cell cycle | 19 | 4.62 × 10−6 | 3.32 × 10−3 |
| GO:0000280 | nuclear division | 10 | 1.99 × 10−5 | 1.42 × 10−2 |
| GO:0007067 | mitosis | 10 | 1.99 × 10−5 | 1.42 × 10−2 |
| GO:0000087 | M phase of mitotic cell cycle | 10 | 2.29 × 10−5 | 1.64 × 10−2 |
| GO:0048285 | organelle fission | 10 | 2.73 × 10−5 | 1.95 × 10−2 |
| GO:0051301 | cell division | 11 | 3.41 × 10−5 | 2.43 × 10−2 |
| GO:0007017 | microtubule-based process | 10 | 5.94 × 10−5 | 4.19 × 10−2 |
| Panel B – genes unique to HeLa synchronization experiment | ||||
| GO:0006259 | DNA metabolic process | 15 | 1.20 × 10−8 | 7.35 × 10−6 |
| GO:0007049 | cell cycle | 17 | 5.65 × 10−8 | 3.45 × 10−5 |
| GO:0006281 | DNA repair | 10 | 2.23 × 10−6 | 1.36 × 10−3 |
| GO:0006974 | response to DNA damage stimulus | 11 | 2.59 × 10−6 | 1.58 × 10−3 |
| GO:0022403 | cell cycle phase | 11 | 6.53 × 10−6 | 3.99 × 10−3 |
| GO:0006260 | DNA replication | 8 | 1.25 × 10−5 | 7.63 × 10−3 |
| GO:0033554 | cellular response to stress | 12 | 1.67 × 10−5 | 1.02 × 10−2 |
| GO:0000278 | mitotic cell cycle | 10 | 1.89 × 10−5 | 1.15 × 10−2 |
| Panel C – overlap of genes of HeLa SORT and synchronization experiments | ||||
| GO:0022403 | cell cycle phase | 46 | 2.21 × 10−49 | 1.40 × 10−46 |
| GO:0000279 | M phase | 43 | 1.12 × 10−48 | 7.09 × 10−46 |
| GO:0000278 | mitotic cell cycle | 44 | 3.69 × 10−48 | 2.33 × 10−45 |
| GO:0022402 | cell cycle process | 48 | 2.39 × 10−46 | 1.51 × 10−43 |
| GO:0007049 | cell cycle | 52 | 6.85 × 10−46 | 4.33 × 10−43 |
| GO:0007067 | mitosis | 37 | 3.87 × 10−45 | 2.45 × 10−42 |
| GO:0000280 | nuclear division | 37 | 3.87 × 10−45 | 2.45 × 10−42 |
| GO:0000087 | M phase of mitotic cell cycle | 37 | 7.76 × 10−45 | 4.90 × 10−42 |
| GO:0048285 | organelle fission | 37 | 1.81 × 10−44 | 1.15 × 10−41 |
| GO:0051301 | cell division | 32 | 3.01 × 10−32 | 1.90 × 10−29 |
| GO:0007017 | microtubule-based process | 23 | 7.87 × 10−21 | 4.97 × 10−18 |
| GO:0000226 | microtubule cytoskeleton organization | 17 | 7.86 × 10−17 | 7.02 × 10−14 |
| GO:0007346 | regulation of mitotic cell cycle | 15 | 8.68 × 10−14 | 5.48 × 10−11 |
| GO:0051726 | regulation of cell cycle | 19 | 1.68 × 10−13 | 1.06 × 10−10 |
| GO:0007051 | spindle organization | 10 | 2.28 × 10−12 | 1.44 × 10-.9 |
| GO:0007059 | chromosome segregation | 11 | 2.02 × 10−11 | 1.28 × 10-.8 |
| GO:0010564 | regulation of cell cycle process | 12 | 2.90 × 10−11 | 1.84 × 10-.8 |
| GO:0007010 | cytoskeleton organization | 18 | 1.70 × 10−10 | 1.08 × 10-.7 |
| GO:0051783 | regulation of nuclear division | 9 | 6.98 × 10−10 | 4.41 × 10-.7 |
| GO:0007088 | regulation of mitosis | 9 | 6.98 × 10−10 | 4.41 × 10-.7 |
| GO:0000070 | mitotic sister chromatid segregation | 8 | 8.88 × 10−10 | 5.61 × 10-.7 |
| GO:0000819 | sister chromatid segregation | 8 | 1.09 × 10-.9 | 6.89 × 10-.7 |
| GO:0051276 | chromosome organization | 17 | 7.07 × 10-.9 | 4.47 × 10-.6 |
| GO:0000075 | cell cycle checkpoint | 9 | 3.58 × 10-.8 | 2.26 × 10-.5 |
| GO:0040001 | establishment of mitotic spindle localization | 5 | 6.00 × 10-.8 | 3.79 × 10-.5 |
| GO:0051656 | establishment of organelle localization | 8 | 9.92 × 10-.8 | 6.27 × 10-.5 |
| GO:0030071 | regulation of mitotic metaphase/anaphase transition | 6 | 1.12 × 10-.7 | 7.07 × 10-.5 |
| GO:0007093 | mitotic cell cycle checkpoint | 7 | 1.23 × 10-.7 | 7.76 × 10-.5 |
| GO:0051653 | spindle localization | 5 | 1.78 × 10-.7 | 1.13 × 10-.4 |
| GO:0051293 | establishment of spindle localization | 5 | 1.78 × 10-.7 | 1.13 × 10-.4 |
| GO:0048015 | phosphoinositide-mediated signaling | 8 | 5.37 × 10-.7 | 3.39 × 10-.4 |
| GO:0008283 | cell proliferation | 14 | 6.95 × 10-.7 | 4.39 × 10-.4 |
| GO:0051640 | organelle localization | 8 | 7.28 × 10-.7 | 4.60 × 10-.4 |
| GO:0007052 | mitotic spindle organization | 5 | 1.14 × 10-.6 | 7.17 × 10-.4 |
| GO:0051329 | interphase of mitotic cell cycle | 8 | 1.57 × 10-.6 | 9.90 × 10-.4 |
| GO:0051325 | interphase | 8 | 1.90 × 10-.6 | 1.20 × 10-.3 |
| GO:0007018 | microtubule-based movement | 8 | 2.92 × 10-.6 | 1.85 × 10-.3 |
| GO:0000910 | cytokinesis | 6 | 2.93 × 10-.6 | 1.85 × 10-.3 |
| GO:0033043 | regulation of organelle organization | 10 | 2.99 × 10-.6 | 1.89 × 10-.3 |
| GO:0010948 | negative regulation of cell cycle process | 5 | 1.01 × 10-.5 | 6.36 × 10-.3 |
| GO:0007094 | mitotic cell cycle spindle assembly checkpoint | 4 | 2.62 × 10-.5 | 1.64 × 10-.2 |
| GO:0045841 | negative regulation of mitotic metaphase/anaphase transition | 4 | 2.62 × 10-.5 | 1.64 × 10-.2 |
| GO:0031577 | spindle checkpoint | 4 | 3.47 × 10-.5 | 2.17 × 10-.2 |
| GO:0045839 | negative regulation of mitosis | 4 | 3.47 × 10-.5 | 2.17 × 10-.2 |
| GO:0051784 | negative regulation of nuclear division | 4 | 3.47 × 10-.5 | 2.17 × 10-.2 |
| GO:0051439 | regulation of ubiquitin-protein ligase activity during mitotic cell cycle | 6 | 4.48 × 10-.5 | 2.79 × 10-.2 |
| GO:0051438 | regulation of ubiquitin-protein ligase activity | 6 | 7.05 × 10-.5 | 4.36 × 10-.2 |
| GO:0051303 | establishment of chromosome localization | 4 | 7.10 × 10-.5 | 4.39 × 10-.2 |
| GO:0050000 | chromosome localization | 4 | 7.10 × 10-.5 | 4.39 × 10-.2 |
Gene lists from the Venn diagram (Fig. 3, Panel a) and Additional file 1: Table S4 were subjected to Gene Ontology term analysis. Genes unique to HeLa SORT experiment (HeLa SORT \ HeLa synchr - Panel A), unique to HeLa synchr experiment (HeLa synchr \ HeLa SORT – Panel B) and the overlap between these two lists (HeLa SORT ∩ HeLa synchr – Panel C) were the input gene lists, respectively
Gene count represents the number of genes from the input list being present in the corresponding GO term. Gene symbols are shown in Additional file 1: Table S5. Only statistical significant (Bonferroni-corrected p-value < 0.05) GO terms are presented. Bold lettered GO terms correspond to unique GO terms found only upon the analysis of either unique HeLa SORT or unique HeLa synchr gene lists