Transcription factors with Perturb-seq knockdown data for PKNOX2-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 = PKNOX2-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 PKNOX2-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 |
|---|---|---|---|---|
| chr11:125,162,861–125,163,059 | 1.5 kb | Proximal (<10kb) | 47 | |
| chr11:125,163,468–125,165,998 | at TSS | At TSS | 417 | |
| chr11:125,166,402–125,167,041 | 1.8 kb | Proximal (<10kb) | 95 | |
| chr11:125,167,297–125,167,601 | 2.7 kb | Proximal (<10kb) | 145 | |
| chr11:125,169,327–125,169,765 | 4.7 kb | Proximal (<10kb) | 49 |
Genomic view of the PKNOX2-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.