Transcription factors with Perturb-seq knockdown data for LINC00504. 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 = LINC00504 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 LINC00504, 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 |
|---|---|---|---|---|
| chr4:13,654,156–13,655,134 | 1233.7 kb | Distal (>10kb) Multiome HiCAR | 499 | |
| chr4:14,764,883–14,765,959 | 122.8 kb | Distal (>10kb) Multiome | 46 | |
| chr4:14,867,382–14,868,405 | 20.2 kb | Distal (>10kb) Multiome | 267 | |
| chr4:15,001,237–15,005,194 | 114.1 kb | Distal (>10kb) Multiome | 997 |
Genomic view of the LINC00504 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.