Transcription factors with Perturb-seq knockdown data for LINC00391. 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 = LINC00391 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 LINC00391, 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 |
|---|---|---|---|---|
| chr13:94,548,604–94,550,382 | 158.9 kb | Distal (>10kb) Multiome | 899 | |
| chr13:94,595,700–94,596,749 | 112.2 kb | Distal (>10kb) Multiome | 741 | |
| chr13:94,601,312–94,602,589 | 106.6 kb | Distal (>10kb) Multiome | 663 | |
| chr13:94,707,389–94,708,611 | 117 bp | At TSS Multiome | 257 | |
| chr13:94,710,520–94,714,056 | 2.8 kb | Proximal (<10kb) Multiome | 498 | |
| chr13:94,717,747–94,718,273 | 9.3 kb | Proximal (<10kb) | 82 | |
| chr13:94,825,487–94,826,097 | 117.3 kb | Distal (>10kb) Multiome | 148 | |
| chr13:94,967,454–94,969,003 | 259.7 kb | Distal (>10kb) Multiome HiCAR | 469 |
Genomic view of the LINC00391 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.