Transcription factors with Perturb-seq knockdown data for LINC01625. 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 = LINC01625 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 LINC01625, 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 |
|---|---|---|---|---|
| chr6:139,473,118–139,473,729 | at TSS | At TSS | 123 | |
| chr6:139,474,373–139,474,654 | 917 bp | At TSS | 201 | |
| chr6:139,477,376–139,478,107 | 3.9 kb | Proximal (<10kb) | 131 | |
| chr6:139,479,537–139,480,038 | 6.1 kb | Proximal (<10kb) | 137 | |
| chr6:139,483,051–139,483,722 | 9.6 kb | Proximal (<10kb) | 172 |
Genomic view of the LINC01625 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.