Transcription factors with Perturb-seq knockdown data for LINC02428. 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 = LINC02428 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 LINC02428, 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 |
|---|---|---|---|---|
| chr4:103,197,655–103,198,939 | 178.6 kb | Distal (>10kb) Multiome | 812 | |
| chr4:103,374,824–103,375,465 | 1.5 kb | Proximal (<10kb) | 116 | |
| chr4:103,429,192–103,430,032 | 52.5 kb | Distal (>10kb) Multiome | 259 | |
| chr4:103,477,555–103,478,976 | 101.4 kb | Distal (>10kb) Multiome | 202 | |
| chr4:103,566,552–103,568,476 | 190.8 kb | Distal (>10kb) Multiome | 361 |
Genomic view of the LINC02428 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.