Transcription factors with Perturb-seq knockdown data for PTPRG-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 = PTPRG-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 PTPRG-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 |
|---|---|---|---|---|
| chr3:60,555,532–60,556,249 | 1763.0 kb | Distal (>10kb) Multiome HiCAR | 181 | |
| chr3:62,318,482–62,319,596 | 130 bp | At TSS Multiome | 488 | |
| chr3:62,368,742–62,369,532 | 50.3 kb | Distal (>10kb) Multiome | 136 | |
| chr3:62,371,938–62,373,044 | 53.7 kb | Distal (>10kb) Multiome | 126 |
Genomic view of the PTPRG-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.