Transcription factors with Perturb-seq knockdown data for LINC02245. 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 = LINC02245 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 LINC02245, 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 |
|---|---|---|---|---|
| chr2:64,767,781–64,768,499 | 288.0 kb | Distal (>10kb) Multiome | 733 | |
| chr2:64,859,294–64,860,146 | 196.4 kb | Distal (>10kb) Multiome | 654 | |
| chr2:64,864,705–64,865,856 | 190.5 kb | Distal (>10kb) Multiome | 538 | |
| chr2:65,049,298–65,049,577 | 6.6 kb | Proximal (<10kb) | 115 | |
| chr2:65,055,719–65,057,013 | 177 bp | At TSS Multiome | 991 | |
| chr2:65,064,806–65,065,005 | 8.6 kb | Proximal (<10kb) | 289 | |
| chr2:65,077,079–65,077,793 | 21.3 kb | Distal (>10kb) Multiome | 133 | |
| chr2:65,129,449–65,131,116 | 74.2 kb | Distal (>10kb) Multiome | 977 | |
| chr2:65,227,140–65,228,436 | 171.6 kb | Distal (>10kb) Multiome | 971 | |
| chr2:65,331,150–65,331,849 | 275.3 kb | Distal (>10kb) Multiome | 47 | |
| chr2:65,350,820–65,351,607 | 295.1 kb | Distal (>10kb) Multiome | 223 |
Genomic view of the LINC02245 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.