Transcription factors with Perturb-seq knockdown data for C9orf40. 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 = C9orf40 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 C9orf40, 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 |
|---|---|---|---|---|
| chr9:74,886,817–74,888,051 | 65.5 kb | Distal (>10kb) Multiome | 583 | |
| chr9:74,951,458–74,953,454 | 15 bp | At TSS Multiome | 1039 | |
| chr9:75,027,251–75,029,154 | 75.5 kb | Distal (>10kb) Multiome | 977 | |
| chr9:75,083,209–75,084,823 | 131.5 kb | Distal (>10kb) Multiome | 427 | |
| chr9:75,086,843–75,089,426 | 135.4 kb | Distal (>10kb) Multiome | 900 |
Genomic view of the C9orf40 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.