Table 2.
Expression of annotated genes in the human and mouse inner ear and spiral ganglion cells.
| Gene | Chr | Pheno-type | Human cochlea | MOUSE | ||
|---|---|---|---|---|---|---|
| Adult hair cells | Spiral ganglion cells | Differential expression in the inner ear? | ||||
| IPP | 1 | H | P | P | P | no |
| GPBP1L1 | 1 | H | P | P | A | no |
| TMEM69 | 1 | H | P | P | A | no |
| MAST2 | 1 | H | M | P | P | Utricle (FC 2.63; FDR 0.819), PN (FC 2.41; FDR 0.977) |
| NASP | 1 | H | P | P | P | no |
| CTH | 1 | L/M | n/a | A | A | — |
| RNU6-1116P | 2 | L/M | n/a | n/a | n/a | — |
| SPTBN1 | 2 | L/M | P | P | P | no |
| EML6 | 2 | L/M | M | A | P | no |
| ILDR1 | 3 | H, L/M | n/a | P | A | HC (FC 7.65; FDR 1.33*10-4) |
| TRIL | 7 | H | n/a | P | P | SC (FC 2.5; FDR 0.243) |
| RP11-32K4.1 | 8 | L/M | n/a | n/a | n/a | — |
| SCUBE2 | 11 | L/M | P | P | P | PN (FC 2.06; FDR 0.927) |
| DOCK9 | 13 | H | M | P | P | HC (FC 3.84; FDR 0.0273), PN (FC 2.24; FDR 0.0549) |
| ISG20 | 15 | L/M | A | P | A | SC (FC 5.88; FDR 0.149); utricle (FC 4.76; FDR 0.353); PN (FC 4.63; FDR 0.514) |
| VPS9D1 | 16 | H | A | P | P | no |
| SPIRE2 | 16 | H | M | P | A | no |
| SHC2 | 19 | L/M | n/a | P | A | HC (FC 6.69; FDR 2.07*10-3) |
| ODF3L2 | 19 | L/M | A | P | n/a | HC (FC 2.40; FDR 0.0485); cochlea (FC 3.38; FDR 0.935); PN (FC 12.04; FDR 0.22) |
| FXYD5 | 19 | L/M | M | A | P | — |
Expression of the 20 annotated genes, as determined by proximity to the top SNP and MAGMA gene set analysis, in the human and mouse auditory system, by associated phenotype. For humans, only cochlear material was available. For mice, data on expression in adult (cochlear) hair cells and spiral ganglion cells (of the cochlear nerve) is listed, as well as differential expression within the inner ear. Abbreviations: H (high frequency phenotype), L/M (low/mid frequency phenotype). Expression in the human cochlea was classified as follows: n/a (not available), A (absent; < 1 fragments per kilobase of exon per million reads mapped (FPKM)), M (marginal; expression > 1 FPKM in 1 tissue sample), P (present; expression > 1 FPKM in more than 1 tissue sample). In mice, expression was investigated within the adult cochlea and spiral ganglion cells. Absent/present labels were designated according to >10.9 expression level or >=50% positive calls, respectively. Differential expression (defined as > 2-fold change) in the inner ear was noted between cell types (hair cells vs supporting cells), tissue types (cochlea vs utricle) and developmental stages (embryonic vs postnatal period). The accompanying fold changes (FC) and false discovery rates (FDR) are mentioned between brackets.