Transcription factors with Perturb-seq knockdown data for LINC01405. 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 = LINC01405 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 LINC01405, 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 |
|---|---|---|---|---|
| chr12:110,688,496–110,690,180 | 247.2 kb | Distal (>10kb) Multiome | 414 | |
| chr12:110,742,238–110,743,370 | 193.6 kb | Distal (>10kb) Multiome | 801 | |
| chr12:110,846,588–110,847,239 | 89.7 kb | Distal (>10kb) Multiome | 371 | |
| chr12:110,936,931–110,937,646 | 659 bp | At TSS Multiome | 373 | |
| chr12:111,033,748–111,035,142 | 98.2 kb | Distal (>10kb) Multiome | 235 |
Genomic view of the LINC01405 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.