Transcription factors with Perturb-seq knockdown data for LINC00475. 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 = LINC00475 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 LINC00475, 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 |
|---|---|---|---|---|
| chr9:92,133,789–92,134,516 | 6.9 kb | Proximal (<10kb) | 252 | |
| chr9:92,137,993–92,138,553 | 2.9 kb | Proximal (<10kb) | 237 | |
| chr9:92,140,183–92,140,786 | 650 bp | At TSS | 418 | |
| chr9:92,141,176–92,141,754 | at TSS | At TSS | 159 |
Genomic view of the LINC00475 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.