Transcription factors with Perturb-seq knockdown data for LINC00641. 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 = LINC00641 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 LINC00641, 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 |
|---|---|---|---|---|
| chr14:20,970,757–20,971,991 | 234.1 kb | Distal (>10kb) Multiome | 745 | |
| chr14:20,989,595–20,990,562 | 215.6 kb | Distal (>10kb) Multiome | 835 | |
| chr14:21,024,660–21,026,214 | 180.4 kb | Distal (>10kb) Multiome | 768 | |
| chr14:21,069,280–21,071,963 | 133.9 kb | Distal (>10kb) Multiome | 899 | |
| chr14:21,092,184–21,093,275 | 112.8 kb | Distal (>10kb) Multiome | 774 | |
| chr14:21,094,184–21,094,833 | 111.0 kb | Distal (>10kb) Multiome | 210 | |
| chr14:21,097,193–21,098,877 | 107.0 kb | Distal (>10kb) Multiome | 469 | |
| chr14:21,103,222–21,104,876 | 101.6 kb | Distal (>10kb) Multiome | 1128 | |
| chr14:21,191,911–21,192,845 | 13.4 kb | Distal (>10kb) Multiome | 463 | |
| chr14:21,203,304–21,204,249 | 1.3 kb | Proximal (<10kb) | 261 | |
| chr14:21,268,822–21,270,154 | 64.2 kb | Distal (>10kb) Multiome | 1029 | |
| chr14:21,308,204–21,309,328 | 103.4 kb | Distal (>10kb) Multiome | 647 | |
| chr14:21,383,896–21,384,850 | 178.8 kb | Distal (>10kb) Multiome | 931 | |
| chr14:21,436,834–21,437,890 | 231.9 kb | Distal (>10kb) Multiome | 875 | |
| chr14:21,455,683–21,456,683 | 250.7 kb | Distal (>10kb) Multiome | 862 | |
| chr14:21,476,573–21,477,687 | 271.5 kb | Distal (>10kb) Multiome | 931 |
Genomic view of the LINC00641 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.