Transcription factors with Perturb-seq knockdown data for LINC00458. 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 = LINC00458 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 LINC00458, 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 |
|---|---|---|---|---|
| chr13:54,126,489–54,127,976 | 4.9 kb | Proximal (<10kb) | 171 | |
| chr13:54,128,111–54,128,827 | 4.0 kb | Proximal (<10kb) | 5 | |
| chr13:54,131,423–54,131,954 | 136.5 kb | Distal (>10kb) Multiome | 93 | |
| chr13:54,132,160–54,132,387 | 478 bp | At TSS | 2 | |
| chr13:54,132,587–54,133,166 | at TSS | At TSS | 36 | |
| chr13:54,266,843–54,268,901 | 374 bp | At TSS Multiome | 301 | |
| chr13:54,269,020–54,269,440 | 809 bp | At TSS | 3 | |
| chr13:54,356,208–54,356,764 | 88.1 kb | Distal (>10kb) Multiome | 88 | |
| chr13:54,402,598–54,404,029 | 135.2 kb | Distal (>10kb) Multiome | 191 | |
| chr13:55,653,252–55,655,582 | 1386.1 kb | Distal (>10kb) Multiome HiCAR | 318 |
Genomic view of the LINC00458 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.