Transcription factors with Perturb-seq knockdown data for DDX59-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 = DDX59-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 DDX59-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 |
|---|---|---|---|---|
| chr1:200,659,319–200,659,583 | 9.9 kb | Proximal (<10kb) | 113 | |
| chr1:200,659,696–200,659,889 | 9.6 kb | Proximal (<10kb) | 20 | |
| chr1:200,665,949–200,666,168 | 3.3 kb | Proximal (<10kb) | 54 | |
| chr1:200,668,644–200,669,109 | 396 bp | At TSS | 68 | |
| chr1:200,669,293–200,670,631 | at TSS | At TSS | 1078 |
Genomic view of the DDX59-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.