Transcription factors with Perturb-seq knockdown data for LINC00598. 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 = LINC00598 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 LINC00598, 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 |
|---|---|---|---|---|
| chr13:40,210,750–40,211,538 | 62.3 kb | Distal (>10kb) Multiome | 30 | |
| chr13:40,232,425–40,233,123 | 40.7 kb | Distal (>10kb) Multiome | 47 | |
| chr13:40,279,819–40,280,554 | 6.6 kb | Proximal (<10kb) Multiome | 43 | |
| chr13:40,309,607–40,310,352 | 36.5 kb | Distal (>10kb) Multiome | 79 | |
| chr13:40,355,207–40,355,904 | 82.0 kb | Distal (>10kb) Multiome | 73 | |
| chr13:40,680,324–40,681,411 | 407.3 kb | Distal (>10kb) Multiome HiCAR | 281 |
Genomic view of the LINC00598 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.