Transcription factors with Perturb-seq knockdown data for CCDC138. 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 = CCDC138 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 CCDC138, 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 |
|---|---|---|---|---|
| chr2:108,533,404–108,535,229 | 252.5 kb | Distal (>10kb) Multiome | 1035 | |
| chr2:108,583,732–108,584,281 | 202.7 kb | Distal (>10kb) Multiome | 283 | |
| chr2:108,608,990–108,609,565 | 177.4 kb | Distal (>10kb) Multiome | 125 | |
| chr2:108,620,806–108,621,587 | 165.5 kb | Distal (>10kb) Multiome | 401 | |
| chr2:108,636,177–108,636,884 | 150.2 kb | Distal (>10kb) Multiome | 398 | |
| chr2:108,718,922–108,720,037 | 67.3 kb | Distal (>10kb) Multiome | 1042 | |
| chr2:108,786,273–108,787,203 | 14 bp | At TSS Multiome | 874 | |
| chr2:109,031,283–109,032,200 | 245.1 kb | Distal (>10kb) Multiome | 570 |
Genomic view of the CCDC138 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.