Table 1.
Enriched GO categories by the shared P6 pRb−/− cochlear and utricular differentially expressed genes by DAVID analysis
| Term | Number of genes | Enrichment score | Fold enrichment | Benjamini p-value | FDR % | Genes |
| cell cycle | 57 | 22.04 | 6.14 | 2.1E-26 | 2.8E-26 | Gmnn, Incenp, Topbp1, Cdc45l, Bub1b, Mcm6, Ccnb2, Myb, Cdc25b, Pola1, Nek2, Chek1, Trip13, Mki67, Spc25, Tacc3, Aspm, Mcm7, Cenpe, Ccnb1, Kif11, Tpx2, Birc5, Cks2, Lig1, Plk1, Haus4, Racgap1, Cdt1, Cdc7, Ccne2, C79407, Mcm2, Prc1, Rb1, LOC100047340, Hells, Rpa1, Cdca8, Gadd45a, Ube2c, Cenpf, Rad51, Skp2, Cdc2a, Cdc6, Syce2, Dscc1, Brca1, Uhrf1, Timeless, Ncapd2, Ccna2, Ccne1, Cdca3, Nusap1, Aurkb |
| microtubule-based process | 14 | 9.16 | 4.48 | 0.00082 | 0.02 | Kif2c, Brca1, Birc5, Tpx2, Kif23, Spc25, Ttll3, Haus4, Gadd45a, Tacc3, Cenpe, Nusap1, Kif22, Kif11 |
| DNA replication | 26 | 7.26 | 12.18 | 5.20E-18 | 5.7E-17 | Ccne2, Mcm5, Mcm2, Cdc45l, Mcm6, Pola1, Tk1, Rpa1, Rfc2, Pold1, Rad51, Rrm2, Mcm7, Pcna, Prim1, Cdc6, Dscc1, Brca1, Cdt1, Mcm4, Dtl, Lig1, Ccne1, Rfc4, Rrm1, Mm.4025.5 |
| response to DNA damage stimulus | 22 | 6.52 | 5.08 | 1.5E-07 | 3.0E-06 | Hmgb2, Brca1, Usp1, Uhrf1, Topbp1, Dtl, Timeless, Lig1, Rad54l, Pola1, Smc5, Rpa1, Chek1, Msh6, Trip13, Ung, Pold1, Gadd45a, Rad51, Cdc2a, Pcna, Kif22 |
| nucleoside binding | 40 | 4.31 | 1.92 | 0.015 | 0.07 | Bub1b, Mcm6, Pola1, Tk1, Nek2, Pbk, Chek1, Trip13, Mcm7, Mcm5, Cenpe, Kif11, Acss2, Mcm4, Pak3, Lig1, Plk1, Dtymk, Msh6, Top2a, Kif22, Fignl1, Kif2c, Cdc7, Mcm2, Hells, Smc5, Rfc2, Ube2c, Rad51, Cdc2a, Rimklb, Cdc6, Chst15, Twf2, Rad54l, Kif23, Rfc4, Rrm1, Aurkb |
| microtubule cytoskeleton organization | 11 | 4.29 | 6.46 | 0.00049 | 0.01 | Brca1, Birc5, Tpx2, Ttll3, Spc25, Haus4, Gadd45a, Tacc3, Cenpe, Nusap1, Kif11 |
| M phase of meiotic cell cycle | 9 | 3.94 | 3.69 | 0.0023 | 0.09 | Trip13, Mki67, Topbp1, Cks2, Rad51, Cdc25b, Syce2, Nek2, Rpa1 |
| interphase of mitotic cell cycle | 8 | 3.37 | 10.55 | 0.00059 | 0.01 | Chek1, Birc5, Gadd45a, Cenpf, Rb1, Skp2, Myb, Pola1 |
| centrosome organization | 4 | 3.16 | 15.21 | 0.069 | 3.29 | Brca1, Haus4, Gadd45a, Kif11 |
| regulation of cell cycle | 14 | 2.43 | 4.33 | 0.0011 | 0.03 | Gmnn, Ccne2, Cdt1, Birc5, Rb1, Chek1, Ccne1, Tacc3, Cenpf, Gadd45a, Cenpe, Skp2, Nusap1, Cdc2a |
| double-strand break repair | 5 | 2 | 7.69 | 0.11 | 6.01 | Trip13, Rad51, Rad54l, Pola1, Rpa1 |
| maintenance of location in cell | 4 | 1.65 | 10.34 | 0.17 | 9.86 | Kdelr3, Tacc3, Aspm, Cenpe |
| chromosome organization | 17 | 1.6 | 2.91 | 0.0092 | 0.38 | Ezh2, Mcm2, Rb1, Hist1h2ad, H2afz, Ncapd2, Rad54l, Mm.104227.1, Hells, Dnmt1, Nek2, Rpa1, Cenpa, Hat1, Top2a, Nusap1, Syce2 |
| cell morphogenesis involved in differentiation | 10 | 1.53 | 3.14 | 0.13 | 7.16 | Tmhs, Mm.209077.1, Krt8, Ntf3, Cdh4, Mm.215838.1, Celsr3, Ptprz1, Isl1, Lhx3 |
| deoxyribonucleotide metabolic process | 4 | 1.17 | 12.93 | 0.1 | 5.29 | Dut, Rrm2, Rrm1, Dtymk |
A majority of genes were upregulated in both P6 pRb−/− utricle and cochlea, with the exception of four genes (Rb1, Gadd45α, Kdelr3, Mm.209077.1) that were downregulated in P6 pRb−/− utricle and cochlea; and four other genes (Ttll3, Mm.4025.5, Mm.104227.1, Mm.215838.1) were downregulated in P6 pRb−/− utricle but upregulated in P6 pRb−/− cochlea.