Transcription factors with Perturb-seq knockdown data for LINC00665. 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 = LINC00665 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 LINC00665, 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 |
|---|---|---|---|---|
| chr19:36,032,424–36,033,187 | 298.9 kb | Distal (>10kb) Multiome | 179 | |
| chr19:36,053,782–36,055,591 | 277.3 kb | Distal (>10kb) Multiome | 1026 | |
| chr19:36,113,981–36,116,196 | 216.5 kb | Distal (>10kb) Multiome | 1052 | |
| chr19:36,127,575–36,128,707 | 203.7 kb | Distal (>10kb) Multiome | 942 | |
| chr19:36,139,425–36,141,811 | 190.4 kb | Distal (>10kb) Multiome | 1037 | |
| chr19:36,160,493–36,161,405 | 170.8 kb | Distal (>10kb) Multiome | 94 | |
| chr19:36,214,162–36,215,543 | 116.9 kb | Distal (>10kb) Multiome | 1008 | |
| chr19:36,245,106–36,245,849 | 86.3 kb | Distal (>10kb) Multiome | 153 | |
| chr19:36,331,415–36,332,377 | 76 bp | At TSS Multiome | 372 | |
| chr19:36,332,804–36,333,055 | 1.1 kb | Proximal (<10kb) | 8 | |
| chr19:36,378,606–36,379,573 | 47.4 kb | Distal (>10kb) Multiome | 839 | |
| chr19:36,418,146–36,419,031 | 86.9 kb | Distal (>10kb) Multiome | 638 | |
| chr19:36,488,856–36,490,274 | 157.9 kb | Distal (>10kb) Multiome | 991 | |
| chr19:36,527,962–36,529,500 | 196.8 kb | Distal (>10kb) Multiome | 937 | |
| chr19:36,572,622–36,573,936 | 241.6 kb | Distal (>10kb) Multiome | 1017 | |
| chr19:36,604,710–36,605,744 | 273.6 kb | Distal (>10kb) Multiome | 657 |
Genomic view of the LINC00665 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.