Transcription factors with Perturb-seq knockdown data for PCGF3-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 = PCGF3-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 PCGF3-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 |
|---|---|---|---|---|
| chr4:498,731–499,543 | 282.7 kb | Distal (>10kb) Multiome | 869 | |
| chr4:575,294–576,132 | 206.4 kb | Distal (>10kb) Multiome | 154 | |
| chr4:663,207–664,324 | 118.1 kb | Distal (>10kb) Multiome | 298 | |
| chr4:673,501–675,336 | 107.5 kb | Distal (>10kb) Multiome | 920 | |
| chr4:680,919–681,550 | 100.5 kb | Distal (>10kb) Multiome | 275 | |
| chr4:688,280–689,636 | 92.6 kb | Distal (>10kb) Multiome | 218 | |
| chr4:705,313–706,398 | 76.2 kb | Distal (>10kb) Multiome | 613 | |
| chr4:781,187–782,732 | 150 bp | At TSS Multiome | 893 | |
| chr4:785,978–786,564 | 4.1 kb | Proximal (<10kb) | 53 | |
| chr4:825,232–826,278 | 43.9 kb | Distal (>10kb) Multiome | 317 | |
| chr4:826,462–827,691 | 45.1 kb | Distal (>10kb) Multiome | 180 | |
| chr4:931,599–932,710 | 150.5 kb | Distal (>10kb) Multiome | 818 | |
| chr4:945,351–946,054 | 163.7 kb | Distal (>10kb) Multiome | 73 | |
| chr4:972,792–974,408 | 191.7 kb | Distal (>10kb) Multiome | 437 | |
| chr4:986,645–987,589 | 205.3 kb | Distal (>10kb) Multiome | 723 | |
| chr4:1,002,360–1,003,561 | 221.3 kb | Distal (>10kb) Multiome | 176 | |
| chr4:1,008,768–1,012,870 | 229.6 kb | Distal (>10kb) Multiome | 793 |
Genomic view of the PCGF3-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.