Table 1. Transcription factors and chromatin modifiers that exhibit significant changes in gene expression upon Atoh1 transduction into human sensory epithelia.
The left column lists gene names followed by gene descriptions. AB T is the average transcript abundance in the Atoh1 treated samples (as FPKMs). AB C is the average abundance in the control samples. LOG2 is the log base2 fold change of Atoh1 transfected compared to the controls. FUNCT indicates whether a given gene is a transcription factor (TF) or a chromatin modifier (CM). Names in bold are genes that show a > 2 fold change in expression (and p<0.05) across all three comparisons (they are part of the 441 differentially expressed genes, see Materials and methods and Results). Genes in plain text show statistically significant changes in all comparisons, but only pass >2 fold in at least one comparison.
| GENE | Description | Ab T | Ab C | LOG2 | Funct |
|---|---|---|---|---|---|
| ATOH1 | atonal bHLH transcription factor 1 | 37.8 | 0.3 | 6.9 | TF |
| RAX | retina and anterior neural fold homeobox | 0.7 | 0.1 | 2.5 | TF |
| ZNF296 | zinc finger protein 296 | 17.1 | 3.0 | 2.5 | TF |
| POU4F3 | POU class 4 homeobox 3 | 3.4 | 0.8 | 2.1 | TF |
| CITED4 | Cbp/p300 interacting transactivator | 56.6 | 13.7 | 2.0 | TF |
| GTF2IRD2 | GTF2I repeat domain containing 2 | 2.7 | 0.7 | 2.0 | TF |
| SNAI1 | snail family transcriptional repressor 1 | 30.7 | 8.9 | 1.8 | TF |
| ZNF775 | zinc finger protein 775 | 17.8 | 5.9 | 1.6 | TF |
| MEF2B | myocyte enhancer factor 2B | 2.1 | 0.7 | 1.6 | TF |
| SOX12 | SRY-box 12 | 10.1 | 3.6 | 1.5 | TF |
| ZNF784 | zinc finger protein 784 | 3.7 | 1.3 | 1.4 | TF |
| ZNF837 | zinc finger protein 837 | 1.8 | 0.7 | 1.4 | TF |
| IRF9 | interferon regulatory factor 9 | 137.3 | 53.5 | 1.4 | TF |
| ZNF692 | zinc finger protein 692 | 36.7 | 15.1 | 1.3 | TF |
| GTF2H3 | general transcription factor IIH subunit 3 | 9.3 | 21.5 | −1.2 | TF |
| ZNF382 | zinc finger protein 382 | 0.9 | 2.2 | −1.2 | TF |
| EP300 | E1A binding protein p300 | 10.9 | 26.3 | −1.3 | CM |
| ZFHX4 | zinc finger homeobox 4 | 1.0 | 2.4 | −1.3 | TF |
| ASH1L | ASH1 like histone lysine methyltransfer | 5.1 | 12.8 | −1.3 | CM |
| ATRX | ATRX, chromatin remodeler | 7.0 | 22.4 | −1.7 | CM |
| SATB2 | SATB homeobox 2 | 0.8 | 3.0 | −1.9 | TF/CM |
| HDAC9 | histone deacetylase 9 | 5.7 | 20.9 | −1.9 | CM |
| TCF19 | transcription factor 19 | 0.7 | 0.2 | 1.8 | TF |
| HES1 | hes family bHLH transcription factor 1 | 78.1 | 24.1 | 1.7 | TF |
| ZNF467 | zinc finger protein 467 | 4.3 | 1.5 | 1.5 | TF |
| GSC | goosecoid homeobox | 0.8 | 0.3 | 1.5 | TF |
| SALL1 | spalt like transcription factor 1 | 9.7 | 3.9 | 1.3 | TF |
| KCNIP3 | potassium voltage-gated channel protein 3 | 10.1 | 4.3 | 1.3 | TF |
| THAP3 | THAP domain containing 3 | 30.6 | 13.2 | 1.2 | TF |
| MSX1 | msh homeobox 1 | 8.4 | 3.7 | 1.2 | TF |
| SCAND1 | SCAN domain containing 1 | 58.9 | 26.8 | 1.1 | TF |
| ING2 | inhibitor of growth family member 2 | 13.2 | 6.1 | 1.1 | CM |
| MLXIP | MLX interacting protein | 8.8 | 4.2 | 1.1 | TF |
| ZNF652 | zinc finger protein 652 | 11.4 | 5.7 | 1.0 | TF |
| PATZ1 | POZ/BTB and AT hook containing zincfinger | 18.1 | 9.3 | 1.0 | TF/CM |
| RARG | retinoic acid receptor gamma | 18.0 | 9.2 | 1.0 | TF |
| GLI4 | GLI family zinc finger 4 | 13.1 | 6.8 | 1.0 | TF |
| THAP8 | THAP domain containing 8 | 7.5 | 4.3 | 0.8 | TF |
| ING5 | inhibitor of growth family member 5 | 17.5 | 10.4 | 0.8 | CM |
| TAF6 | TATA-box binding protein associated factor | 42.6 | 26.1 | 0.7 | TF |
| ZNF768 | zinc finger protein 768 | 47.2 | 29.3 | 0.7 | TF |
| CREBBP | CREB binding protein | 11.6 | 21.8 | −0.9 | TF |