Transcription factors with Perturb-seq knockdown data for LINC02235. 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 = LINC02235 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 LINC02235, 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 |
|---|---|---|---|---|
| chr8:81,630,496–81,631,299 | 211.6 kb | Distal (>10kb) Multiome | 326 | |
| chr8:81,685,772–81,686,622 | 156.3 kb | Distal (>10kb) Multiome | 915 | |
| chr8:81,720,515–81,721,822 | 121.3 kb | Distal (>10kb) Multiome | 750 | |
| chr8:81,731,713–81,733,032 | 109.9 kb | Distal (>10kb) Multiome | 732 | |
| chr8:81,895,652–81,897,396 | 53.6 kb | Distal (>10kb) Multiome | 316 | |
| chr8:81,897,889–81,899,280 | 55.6 kb | Distal (>10kb) Multiome | 138 | |
| chr8:81,903,428–81,904,466 | 61.2 kb | Distal (>10kb) Multiome | 155 | |
| chr8:81,912,367–81,913,089 | 70.1 kb | Distal (>10kb) Multiome | 113 |
Genomic view of the LINC02235 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.