Transcription factors with Perturb-seq knockdown data for CBR4-DT. 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 = CBR4-DT 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 CBR4-DT, 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 |
|---|---|---|---|---|
| chr4:169,005,268–169,005,969 | 4.5 kb | Proximal (<10kb) | 186 | |
| chr4:169,009,429–169,010,942 | at TSS | At TSS | 829 | |
| chr4:169,015,982–169,016,952 | 5.6 kb | Proximal (<10kb) | 314 | |
| chr4:169,017,814–169,018,427 | 7.4 kb | Proximal (<10kb) | 110 |
Genomic view of the CBR4-DT 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.