Transcription factors with Perturb-seq knockdown data for OTX2-AS1. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = OTX2-AS1 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of OTX2-AS1, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.
| Accessibility | Element | Dist. to TSS | Link type | TFs |
|---|---|---|---|---|
| chr14:56,552,658–56,553,598 | 260.3 kb | Distal (>10kb) Multiome | 60 | |
| chr14:56,579,396–56,580,264 | 233.5 kb | Distal (>10kb) Multiome | 723 | |
| chr14:56,657,366–56,658,170 | 155.4 kb | Distal (>10kb) Multiome | 55 | |
| chr14:56,659,300–56,659,979 | 153.5 kb | Distal (>10kb) Multiome | 126 | |
| chr14:56,794,034–56,795,658 | 18.7 kb | Distal (>10kb) Multiome | 177 | |
| chr14:56,797,476–56,799,717 | 14.2 kb | Distal (>10kb) Multiome | 305 | |
| chr14:56,804,880–56,806,970 | 7.4 kb | Proximal (<10kb) Multiome | 343 | |
| chr14:56,808,566–56,809,371 | 4.2 kb | Proximal (<10kb) Multiome | 138 | |
| chr14:56,810,408–56,810,605 | 2.6 kb | Proximal (<10kb) | 43 | |
| chr14:56,811,355–56,811,797 | 1.4 kb | Proximal (<10kb) | 46 | |
| chr14:56,811,966–56,812,705 | 477 bp | At TSS | 105 | |
| chr14:56,816,623–56,818,130 | 3.4 kb | Proximal (<10kb) | 186 | |
| chr14:56,846,930–56,847,795 | 34.1 kb | Distal (>10kb) Multiome HiCAR | 173 | |
| chr14:56,855,868–56,856,570 | 43.0 kb | Distal (>10kb) Multiome HiCAR | 256 | |
| chr14:56,858,307–56,858,852 | 45.5 kb | Distal (>10kb) Multiome HiCAR | 104 | |
| chr14:56,998,512–56,999,273 | 185.7 kb | Distal (>10kb) Multiome HiCAR | 139 | |
| chr14:57,049,791–57,050,396 | 236.9 kb | Distal (>10kb) Multiome HiCAR | 43 |
Genomic view of the OTX2-AS1 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.