Transcription factors with Perturb-seq knockdown data for PAXX. 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 = PAXX 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 PAXX, 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 |
|---|---|---|---|---|
| chr9:136,711,795–136,713,743 | 280.0 kb | Distal (>10kb) Multiome | 459 | |
| chr9:136,727,616–136,729,079 | 264.2 kb | Distal (>10kb) Multiome | 1013 | |
| chr9:136,762,846–136,763,902 | 229.2 kb | Distal (>10kb) Multiome | 271 | |
| chr9:136,788,889–136,789,680 | 203.1 kb | Distal (>10kb) Multiome | 351 | |
| chr9:136,790,433–136,792,285 | 201.3 kb | Distal (>10kb) Multiome | 864 | |
| chr9:136,798,823–136,801,421 | 191.1 kb | Distal (>10kb) Multiome | 874 | |
| chr9:136,807,251–136,808,764 | 184.5 kb | Distal (>10kb) Multiome | 714 | |
| chr9:136,842,325–136,842,872 | 149.9 kb | Distal (>10kb) Multiome | 492 | |
| chr9:136,846,187–136,850,214 | 143.0 kb | Distal (>10kb) Multiome | 1074 | |
| chr9:136,865,842–136,866,772 | 126.0 kb | Distal (>10kb) Multiome | 742 | |
| chr9:136,885,976–136,887,547 | 106.0 kb | Distal (>10kb) Multiome | 770 | |
| chr9:136,943,250–136,945,621 | 47.7 kb | Distal (>10kb) Multiome | 883 | |
| chr9:136,949,631–136,950,846 | 42.2 kb | Distal (>10kb) Multiome | 776 | |
| chr9:136,977,106–136,980,430 | 13.9 kb | Distal (>10kb) Multiome | 413 | |
| chr9:136,985,053–136,985,479 | 6.9 kb | Proximal (<10kb) | 81 | |
| chr9:136,991,827–136,993,248 | 83 bp | At TSS Multiome | 720 | |
| chr9:136,994,459–136,995,164 | 2.0 kb | Proximal (<10kb) | 140 | |
| chr9:137,027,536–137,029,054 | 35.8 kb | Distal (>10kb) Multiome | 539 | |
| chr9:137,029,231–137,029,652 | 37.1 kb | Distal (>10kb) Multiome | 386 | |
| chr9:137,045,334–137,046,838 | 54.1 kb | Distal (>10kb) Multiome | 829 | |
| chr9:137,053,352–137,054,892 | 61.7 kb | Distal (>10kb) Multiome | 544 | |
| chr9:137,067,810–137,068,494 | 75.7 kb | Distal (>10kb) Multiome | 492 | |
| chr9:137,069,879–137,071,138 | 78.2 kb | Distal (>10kb) Multiome | 703 | |
| chr9:137,076,758–137,078,723 | 85.0 kb | Distal (>10kb) Multiome | 530 | |
| chr9:137,085,844–137,087,716 | 94.5 kb | Distal (>10kb) Multiome | 890 | |
| chr9:137,129,244–137,130,499 | 137.4 kb | Distal (>10kb) Multiome | 823 | |
| chr9:137,167,984–137,170,155 | 177.1 kb | Distal (>10kb) Multiome | 560 | |
| chr9:137,188,099–137,189,538 | 196.3 kb | Distal (>10kb) Multiome | 954 | |
| chr9:137,200,175–137,201,689 | 208.5 kb | Distal (>10kb) Multiome | 856 | |
| chr9:137,205,371–137,205,975 | 213.2 kb | Distal (>10kb) Multiome | 758 | |
| chr9:137,221,373–137,224,294 | 229.5 kb | Distal (>10kb) Multiome | 843 | |
| chr9:137,227,249–137,228,051 | 235.3 kb | Distal (>10kb) Multiome | 533 | |
| chr9:137,236,161–137,237,143 | 244.2 kb | Distal (>10kb) Multiome | 748 | |
| chr9:137,239,991–137,242,933 | 248.6 kb | Distal (>10kb) Multiome | 1117 | |
| chr9:137,243,659–137,245,307 | 251.9 kb | Distal (>10kb) Multiome | 471 | |
| chr9:137,253,801–137,256,036 | 262.9 kb | Distal (>10kb) Multiome | 843 | |
| chr9:137,280,593–137,281,861 | 288.8 kb | Distal (>10kb) Multiome | 223 |
Genomic view of the PAXX 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.