Transcription factors with Perturb-seq knockdown data for LINC02422. 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 = LINC02422 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 LINC02422, 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 |
|---|---|---|---|---|
| chr12:31,659,057–31,659,786 | 300.0 kb | Distal (>10kb) Multiome HiCAR | 737 | |
| chr12:31,728,407–31,729,774 | 230.2 kb | Distal (>10kb) Multiome HiCAR | 938 | |
| chr12:31,749,119–31,749,785 | 209.9 kb | Distal (>10kb) Multiome | 885 | |
| chr12:31,896,572–31,897,018 | 62.5 kb | Distal (>10kb) Multiome | 385 | |
| chr12:31,958,831–31,959,907 | 45 bp | At TSS Multiome | 866 | |
| chr12:31,962,116–31,962,481 | 2.8 kb | Proximal (<10kb) | 33 | |
| chr12:31,966,416–31,967,293 | 7.5 kb | Proximal (<10kb) Multiome | 118 | |
| chr12:32,047,438–32,048,247 | 88.6 kb | Distal (>10kb) Multiome | 272 | |
| chr12:32,106,218–32,107,295 | 147.4 kb | Distal (>10kb) Multiome | 874 | |
| chr12:32,139,428–32,140,190 | 180.6 kb | Distal (>10kb) Multiome | 274 |
Genomic view of the LINC02422 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.