Transcription factors with Perturb-seq knockdown data for LNCPRESS2. 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 = LNCPRESS2 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 LNCPRESS2, 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 |
|---|---|---|---|---|
| chr4:92,252,855–92,255,716 | 22.0 kb | Distal (>10kb) Multiome | 299 | |
| chr4:92,255,961–92,257,467 | 20.5 kb | Distal (>10kb) Multiome | 302 | |
| chr4:92,270,988–92,271,952 | 5.1 kb | Proximal (<10kb) | 166 | |
| chr4:92,273,895–92,274,530 | 2.5 kb | Proximal (<10kb) | 18 | |
| chr4:92,274,632–92,275,690 | 1.4 kb | Proximal (<10kb) | 67 | |
| chr4:92,276,796–92,277,904 | 393 bp | At TSS Multiome | 174 | |
| chr4:92,303,594–92,304,497 | 26.8 kb | Distal (>10kb) Multiome | 190 | |
| chr4:92,304,776–92,306,402 | 28.6 kb | Distal (>10kb) Multiome | 370 | |
| chr4:92,433,090–92,433,831 | 156.5 kb | Distal (>10kb) Multiome HiCAR | 108 | |
| chr4:92,438,845–92,439,507 | 162.1 kb | Distal (>10kb) Multiome HiCAR | 90 | |
| chr4:92,443,611–92,444,707 | 167.3 kb | Distal (>10kb) Multiome HiCAR | 153 | |
| chr4:92,520,410–92,520,980 | 243.6 kb | Distal (>10kb) Multiome | 189 |
Genomic view of the LNCPRESS2 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.