Transcription factors with Perturb-seq knockdown data for SPEN-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 = SPEN-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 SPEN-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 |
|---|---|---|---|---|
| chr1:15,584,405–15,585,197 | 263.4 kb | Distal (>10kb) Multiome | 693 | |
| chr1:15,603,163–15,603,936 | 244.5 kb | Distal (>10kb) Multiome | 795 | |
| chr1:15,616,785–15,618,260 | 230.8 kb | Distal (>10kb) Multiome | 909 | |
| chr1:15,676,618–15,677,408 | 171.0 kb | Distal (>10kb) Multiome | 95 | |
| chr1:15,741,258–15,741,859 | 106.6 kb | Distal (>10kb) Multiome | 436 | |
| chr1:15,757,615–15,759,609 | 89.6 kb | Distal (>10kb) Multiome | 439 | |
| chr1:15,799,931–15,800,776 | 47.8 kb | Distal (>10kb) Multiome | 734 | |
| chr1:15,834,229–15,836,682 | 12.1 kb | Distal (>10kb) Multiome | 1154 | |
| chr1:15,847,036–15,848,900 | 490 bp | At TSS Multiome | 817 | |
| chr1:15,849,314–15,850,241 | 1.5 kb | Proximal (<10kb) Multiome | 788 | |
| chr1:15,975,319–15,976,269 | 127.7 kb | Distal (>10kb) Multiome | 788 | |
| chr1:16,012,632–16,013,679 | 165.0 kb | Distal (>10kb) Multiome | 615 | |
| chr1:16,026,326–16,027,360 | 178.7 kb | Distal (>10kb) Multiome | 186 | |
| chr1:16,032,851–16,033,317 | 184.9 kb | Distal (>10kb) Multiome | 349 | |
| chr1:16,048,527–16,049,209 | 200.6 kb | Distal (>10kb) Multiome | 288 | |
| chr1:16,073,117–16,073,908 | 225.4 kb | Distal (>10kb) Multiome | 375 | |
| chr1:16,115,357–16,116,733 | 267.9 kb | Distal (>10kb) Multiome | 269 | |
| chr1:16,145,972–16,147,046 | 298.3 kb | Distal (>10kb) Multiome | 689 |
Genomic view of the SPEN-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.