Transcription factors with Perturb-seq knockdown data for PTPN23-DT. 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 = PTPN23-DT 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 PTPN23-DT, 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 |
|---|---|---|---|---|
| chr3:47,008,983–47,010,119 | 372.0 kb | Distal (>10kb) Multiome HiCAR | 328 | |
| chr3:47,163,333–47,164,907 | 217.4 kb | Distal (>10kb) Multiome | 981 | |
| chr3:47,281,636–47,283,234 | 98.8 kb | Distal (>10kb) Multiome | 941 | |
| chr3:47,380,120–47,381,966 | 608 bp | At TSS Multiome | 1058 | |
| chr3:47,475,384–47,476,386 | 94.4 kb | Distal (>10kb) Multiome | 967 | |
| chr3:47,512,910–47,514,044 | 132.1 kb | Distal (>10kb) Multiome | 892 | |
| chr3:47,522,175–47,522,702 | 140.8 kb | Distal (>10kb) Multiome | 591 | |
| chr3:47,577,493–47,579,738 | 197.8 kb | Distal (>10kb) Multiome | 446 |
Genomic view of the PTPN23-DT 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.