Transcription factors with Perturb-seq knockdown data for LINC01416. 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 = LINC01416 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 LINC01416, 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 |
|---|---|---|---|---|
| chr18:55,747,941–55,749,345 | 249.7 kb | Distal (>10kb) Multiome | 394 | |
| chr18:55,903,416–55,904,687 | 94.2 kb | Distal (>10kb) Multiome | 222 | |
| chr18:55,998,099–55,998,677 | at TSS | At TSS | 109 | |
| chr18:56,002,904–56,003,602 | 4.7 kb | Proximal (<10kb) | 24 |
Genomic view of the LINC01416 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.