Transcription factors with Perturb-seq knockdown data for USP38-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 = USP38-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 USP38-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 |
|---|---|---|---|---|
| chr4:141,220,251–141,221,612 | 1963.9 kb | Distal (>10kb) Multiome HiCAR | 812 | |
| chr4:143,184,075–143,186,098 | 30 bp | At TSS Multiome | 949 | |
| chr4:143,308,285–143,308,784 | 123.8 kb | Distal (>10kb) Multiome | 88 | |
| chr4:143,335,478–143,338,231 | 152.2 kb | Distal (>10kb) Multiome | 941 |
Genomic view of the USP38-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.