Transcription factors with Perturb-seq knockdown data for PXN-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 = PXN-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 PXN-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 |
|---|---|---|---|---|
| chr12:119,988,471–119,990,364 | 211.2 kb | Distal (>10kb) Multiome | 892 | |
| chr12:120,086,807–120,087,619 | 114.1 kb | Distal (>10kb) Multiome | 957 | |
| chr12:120,093,667–120,094,287 | 107.2 kb | Distal (>10kb) Multiome | 172 | |
| chr12:120,116,125–120,117,765 | 84.4 kb | Distal (>10kb) Multiome | 903 | |
| chr12:120,194,328–120,196,208 | 6.5 kb | Proximal (<10kb) Multiome | 1032 | |
| chr12:120,200,671–120,201,921 | 16 bp | At TSS Multiome | 1006 | |
| chr12:120,228,170–120,231,900 | 27.3 kb | Distal (>10kb) Multiome HiCAR | 1050 | |
| chr12:120,265,150–120,266,362 | 64.5 kb | Distal (>10kb) Multiome HiCAR | 617 | |
| chr12:120,290,301–120,293,526 | 91.9 kb | Distal (>10kb) Multiome | 1338 | |
| chr12:120,302,138–120,302,609 | 101.0 kb | Distal (>10kb) Multiome | 711 | |
| chr12:120,317,215–120,317,997 | 116.4 kb | Distal (>10kb) Multiome | 872 | |
| chr12:120,361,277–120,362,299 | 160.5 kb | Distal (>10kb) Multiome | 308 | |
| chr12:120,368,637–120,370,303 | 167.9 kb | Distal (>10kb) Multiome | 250 | |
| chr12:120,388,762–120,389,560 | 187.9 kb | Distal (>10kb) Multiome | 178 | |
| chr12:120,394,470–120,395,052 | 193.5 kb | Distal (>10kb) Multiome | 283 | |
| chr12:120,413,842–120,414,516 | 212.9 kb | Distal (>10kb) Multiome | 289 | |
| chr12:120,437,436–120,438,568 | 236.7 kb | Distal (>10kb) Multiome | 725 | |
| chr12:120,445,927–120,446,970 | 245.2 kb | Distal (>10kb) Multiome | 982 | |
| chr12:120,468,864–120,470,390 | 268.5 kb | Distal (>10kb) Multiome | 942 | |
| chr12:120,495,362–120,496,939 | 294.7 kb | Distal (>10kb) Multiome | 794 |
Genomic view of the PXN-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.