Transcription factors with Perturb-seq knockdown data for PKN2-AS1. 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 = PKN2-AS1 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 PKN2-AS1, 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 |
|---|---|---|---|---|
| chr1:88,462,321–88,463,295 | 222.1 kb | Distal (>10kb) Multiome | 334 | |
| chr1:88,662,071–88,663,175 | 22.4 kb | Distal (>10kb) Multiome | 148 | |
| chr1:88,683,036–88,685,546 | 786 bp | At TSS Multiome | 961 | |
| chr1:88,890,883–88,892,134 | 206.6 kb | Distal (>10kb) Multiome | 949 |
Genomic view of the PKN2-AS1 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.