Transcription factors with Perturb-seq knockdown data for LINC03059. 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 = LINC03059 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 LINC03059, 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 |
|---|---|---|---|---|
| chr14:56,804,880–56,806,970 | 306.9 kb | Distal (>10kb) Multiome HiCAR | 343 | |
| chr14:56,846,930–56,847,795 | 265.3 kb | Distal (>10kb) Multiome | 173 | |
| chr14:56,855,868–56,856,570 | 256.5 kb | Distal (>10kb) Multiome | 256 | |
| chr14:56,858,307–56,858,852 | 254.0 kb | Distal (>10kb) Multiome | 104 | |
| chr14:56,998,512–56,999,273 | 113.8 kb | Distal (>10kb) Multiome | 139 | |
| chr14:57,049,791–57,050,396 | 62.6 kb | Distal (>10kb) Multiome | 43 | |
| chr14:57,060,261–57,060,970 | 7.6 kb | Proximal (<10kb) | 180 | |
| chr14:57,066,982–57,067,221 | 1.3 kb | Proximal (<10kb) | 178 | |
| chr14:57,068,510–57,068,949 | at TSS | At TSS | 44 | |
| chr14:57,069,822–57,070,031 | 1.3 kb | Proximal (<10kb) | 40 | |
| chr14:57,268,159–57,269,344 | 156.0 kb | Distal (>10kb) Multiome | 916 | |
| chr14:57,364,988–57,365,748 | 252.6 kb | Distal (>10kb) Multiome | 54 | |
| chr14:57,389,614–57,391,598 | 277.8 kb | Distal (>10kb) Multiome | 779 |
Genomic view of the LINC03059 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.