Table 2 Comparison of over-represented GO terms between parent genes of the retrocopies and the retrocopy-overlapped genes
From: Evolutionary fate and implications of retrocopies in the African coelacanth genome
Category | GO.ID | Term | Annotated | Significant | Expected | classicFisher | |
|---|---|---|---|---|---|---|---|
Parent gene | BP | GO:0006278 | RNA-dependent DNA replication | 241 | 24 | 5.69 | 2.20E-09 |
Parent gene | BP | GO:0015074 | DNA integration | 76 | 13 | 1.8 | 2.10E-08 |
Parent gene | BP | GO:0006260 | DNA replication | 314 | 25 | 7.42 | 9.30E-08 |
Parent gene | BP | GO:0006259 | DNA metabolic process | 555 | 32 | 13.11 | 2.30E-06 |
Parent gene | BP | GO:0044260 | cellular macromolecule metabolic process | 3332 | 103 | 78.72 | 0.0005 |
Parent gene | BP | GO:0034645 | cellular macromolecule biosynthetic process | 1763 | 62 | 41.65 | 0.00051 |
Parent gene | BP | GO:0009059 | macromolecule biosynthetic process | 1772 | 62 | 41.86 | 0.00058 |
Parent gene | BP | GO:0044237 | cellular metabolic process | 4497 | 130 | 106.24 | 0.00092 |
Parent gene | BP | GO:0044267 | cellular protein metabolic process | 1574 | 55 | 37.19 | 0.00136 |
Parent gene | BP | GO:0044249 | cellular biosynthetic process | 2068 | 66 | 48.86 | 0.00419 |
Parent gene | BP | GO:1901576 | organic substance biosynthetic process | 2108 | 66 | 49.8 | 0.00663 |
Parent gene | BP | GO:0043170 | macromolecule metabolic process | 3799 | 108 | 89.75 | 0.00792 |
Retrocopy-overlapped gene | BP | GO:0006811 | ion transport | 592 | 21 | 6.84 | 3.40E-06 |
Retrocopy-overlapped gene | BP | GO:0044765 | single-organism transport | 1074 | 27 | 12.41 | 6.70E-05 |
Retrocopy-overlapped gene | BP | GO:0006810 | transport | 1617 | 34 | 18.68 | 0.00023 |
Retrocopy-overlapped gene | BP | GO:0051234 | establishment of localization | 1631 | 34 | 18.85 | 0.00027 |
Parent gene | CC | GO:0005840 | ribosome | 151 | 9 | 3.34 | 0.0061 |
Parent gene | CC | GO:0005737 | cytoplasm | 1294 | 41 | 28.61 | 0.0081 |
Parent gene | CC | GO:0044456 | synapse part | 83 | 6 | 1.83 | 0.0099 |
Retrocopy-overlapped gene | CC | GO:0044425 | membrane part | 2692 | 43 | 31.71 | 0.0073 |
Retrocopy-overlapped gene | CC | GO:0016021 | integral component of membrane | 2478 | 40 | 29.19 | 0.0091 |
Parent gene | MF | GO:0003676 | nucleic acid binding | 2867 | 158 | 77.88 | 1.50E-21 |
Parent gene | MF | GO:1901363 | heterocyclic compound binding | 4595 | 202 | 124.81 | 6.60E-17 |
Parent gene | MF | GO:0097159 | organic cyclic compound binding | 4608 | 202 | 125.17 | 9.30E-17 |
Parent gene | MF | GO:0046983 | protein dimerization activity | 419 | 35 | 11.38 | 3.40E-09 |
Parent gene | MF | GO:0003964 | RNA-directed DNA polymerase activity | 241 | 24 | 6.55 | 4.20E-08 |
Parent gene | MF | GO:0034061 | DNA polymerase activity | 262 | 25 | 7.12 | 5.00E-08 |
Parent gene | MF | GO:0003723 | RNA binding | 528 | 36 | 14.34 | 3.60E-07 |
Parent gene | MF | GO:0016779 | nucleotidyltransferase activity | 319 | 25 | 8.67 | 2.10E-06 |
Parent gene | MF | GO:0005488 | binding | 10088 | 298 | 274.02 | 0.002 |
Parent gene | MF | GO:0016772 | transferase activity, transferring phosphorus-containing groups | 1051 | 43 | 28.55 | 0.0045 |
Retrocopy-overlapped gene | MF | GO:0015075 | ion transmembrane transporter activity | 594 | 22 | 8.11 | 2.00E-05 |
Retrocopy-overlapped gene | MF | GO:0022891 | substrate-specific transmembrane transport | 623 | 22 | 8.51 | 4.20E-05 |
Retrocopy-overlapped gene | MF | GO:0022892 | substrate-specific transporter activity | 688 | 23 | 9.39 | 6.40E-05 |
Retrocopy-overlapped gene | MF | GO:0022857 | transmembrane transporter activity | 706 | 23 | 9.64 | 9.50E-05 |
Retrocopy-overlapped gene | MF | GO:0008324 | cation transmembrane transporter activity | 426 | 16 | 5.82 | 0.00025 |
Retrocopy-overlapped gene | MF | GO:0005215 | transporter activity | 877 | 25 | 11.98 | 0.00037 |