Transcription factors with Perturb-seq knockdown data for C9orf43. 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 = C9orf43 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 C9orf43, 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 |
|---|---|---|---|---|
| chr9:113,400,912–113,402,007 | 8.7 kb | Proximal (<10kb) | 859 | |
| chr9:113,407,014–113,407,193 | 3.5 kb | Proximal (<10kb) | 198 | |
| chr9:113,409,973–113,410,921 | at TSS | At TSS | 997 | |
| chr9:113,411,042–113,411,193 | 301 bp | At TSS | 293 | |
| chr9:113,411,295–113,411,475 | 554 bp | At TSS | 65 |
Genomic view of the C9orf43 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.