Transcription factors with Perturb-seq knockdown data for CASC9. 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 = CASC9 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 CASC9, 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 |
|---|---|---|---|---|
| chr8:75,218,930–75,219,813 | 105.2 kb | Distal (>10kb) Multiome | 168 | |
| chr8:75,324,205–75,324,787 | at TSS | At TSS | 101 | |
| chr8:75,403,673–75,405,178 | 79.9 kb | Distal (>10kb) Multiome | 216 | |
| chr8:75,406,715–75,408,554 | 82.7 kb | Distal (>10kb) Multiome | 947 |
Genomic view of the CASC9 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.