TABLE 4.
Examples of signature genes
| Gene description | Symbol | Entrez | Fold change (and pattern) |
|---|---|---|---|
| Carbonic anhydrase 13 | Car13 | 71934 | 3.3 (C) |
| Carboxylesterase 3 | Ces3 | 104158 | 11.2 (C) |
| Clusterin | Clu | 12759 | 17.1 (C) |
| Cytochrome P450, family 26, subfamily a, polypeptide 1 | Cyp26A1 | 13082 | 18.1 (C) |
| Endothelin converting enzyme-like 1 | Ecel1 | 13599 | 3.3 (C) |
| ES cell derived homeobox | Ehox | 194856 | 5.0 (C) |
| Forkhead box G1 | FoxG1 | 15228 | 6.3 (C) |
| Follistatin | Fst | 14313 | 26.2 (C) |
| GATA binding protein 3 | Gata3 | 14462 | 13.1 (C) |
| Gap junction membrane channel protein β 2 | Gjb2 | 14619 | 5.9 (C) |
| Hairy/enhancer of split related with YRPW motif 2 | Hey2 | 15214 | 3.0 (C) |
| High mobility group AT-hook 2 | Hmga2 | 15364 | 5.1 (C) |
| Iroquois related homeobox 3 (Drosophila) | Irx3 | 16373 | 9.5 (C) |
| Iroquois related homeobox 5 (Drosophila) | Irx5 | 54352 | 6.7 (C) |
| Solute carrier family 29 (nucleoside transporters), member 1 | Slc29A1 | 63959 | 4.0 (C) |
| Solute carrier family 39 (metal ion transporter), member 8 | Slc39A8 | 67547 | 9.1 (C) |
| Solute carrier family 7 (cationic amino acid transporter, y+ system), member 10 | Slc7A10 | 53896 | 4.4 (C) |
| Tachykinin 1 | Tac1 | 21333 | 36.1 (C) |
| Vascular endothelial growth factor C | Vegfc | 22341 | 5.6 (C) |
| Wingless-related MMTV integration site 7A | Wnt7a | 22421 | 3.1 (C) |
| Apolipoprotein B editing complex 2 | Apobec2 | 11811 | 23.4 (U) |
| BMP and activin membrane-bound inhibitor homolog (Xenopus laevis) | Bambi | 68010 | 6.4 (U) |
| Bone morphogenetic protein 2 | Bmp2 | 12156 | 7.6 (U) |
| Bone morphogenetic protein 6 | Bmp6 | 12161 | 4.7 (U) |
| Calcium channel, voltage-dependent, α-2, δ-subunit 3 | Cacna2D3 | 12294 | 6.5 (U) |
| Cyclin D2 | Ccnd2 | 12444 | 3.1 (U) |
| CEA-related cell adhesion molecule 10 | Ceacam10 | 26366 | 3.6 (U) |
| Claudin 11 | Cldn11 | 18417 | 3.2 (U) |
| Claudin 8 | Cldn8 | 54420 | 8.1 (U) |
| Procollagen, type XIV, α 1 | Col14A1 | 12818 | 3.6 (U) |
| Distal-less homeobox 1 (Dlx1) | Dlx1 | 13390 | 27.5 (U) |
| Forkhead box P1 | FoxP1 | 108655 | 3.1 (U) |
| Glutamate receptor, ionotropic, AMPA2 (α-2) | Gria2 | 14800 | 17.8 (U) |
| Glutamate receptor, ionotropic, kainate 1 | Grik1 | 14805 | 3.5 (U) |
| Hairy and enhancer of split 5 (Drosophila) | Hes5 | 15208 | 8.7 (U) |
| Homer homolog 2 (Drosophila) | Homer2 | 26557 | 4.3 (U) |
| Potassium voltage-gated channel, Shal-related family, member 2 | Kcnd2 | 16508 | 22.9 (U) |
| Protocadherin 20 | Pcdh20 | 219257 | 3.5 (U) |
| Parathyroid hormone-like peptide | Pthlh | 19227 | 18.8 (U) |
| T-box 3 | Tbx3 | 21386 | 7.0 (U) |
| Carbonic anyhydrase 12 | Car12 | 76459 | 6.6 (S) |
| Cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) | Cdkn2B | 12579 | 5.7 (S) |
| Procollagen, type III, α-1 | Col3A1 | 12825 | 3.0 (S) |
| Chemokine (C-X-C motif) ligand 12 | Cxcl12 | 20315 | 4.3 (S) |
| Forkhead box D1 | FoxD1 | 15229 | 3.6 (S) |
| LIM homeobox protein 1 | Lhx1 | 16869 | 6.3 (S) |
| Mesenchyme homeobox 2 | Meox2 | 17286 | 3.7 (S) |
| Membrane metallo endopeptidase | Mme | 17380 | 3.4 (S) |
| Myosin 1H | Myo1H | 231646 | 6.5 (S) |
| Nidogen 1 | Nid1 | 18073 | 3.1 (S) |
| Otoancorin | Otoa | 246190 | 9.0 (S) |
| PDZ domain containing RING finger 3 | Pdzrn3 | 55983 | 9.1 (S) |
| Retinoic acid receptor, β | Rarb | 218772 | 4.7 (S) |
| Receptor tyrosine kinase-like orphan receptor 2 | Ror2 | 26564 | 3.0 (S) |
| Sal-like 3 (Drosophila) | Sall3 | 20689 | 3.2 (S) |
| Solute carrier family 6 (neurotransmitter transporter), member 14 | Slc6A14 | 56774 | 6.5 (S) |
| SPARC related modular calcium binding 1 | Smoc1 | 64075 | 4.8 (S) |
| Tachykinin receptor 3 | Tacr3 | 21338 | 13.6 (S) |
| Vav 3 oncogene | Vav3 | 57257 | 5.0 (S) |
| Zinc finger protein of the cerebellum 1 | Zic1 | 22771 | 3.7 (S) |
A sample of twenty genes from each of the Cochlea (C), Utricle (U), and Saccule (S) patterns of distinctive (signature) gene expression. Supplemental Table 4 lists all of the genes in these (and other) patterns that were upregulated by ≥1.5-fold.