Transcription factors with Perturb-seq knockdown data for LINC00938. 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 = LINC00938 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 LINC00938, 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 |
|---|---|---|---|---|
| chr12:45,725,008–45,725,200 | 2.7 kb | Proximal (<10kb) | 21 | |
| chr12:45,726,865–45,728,208 | 239 bp | At TSS Multiome | 991 | |
| chr12:45,728,446–45,731,126 | 1.2 kb | Proximal (<10kb) Multiome | 1023 | |
| chr12:45,989,594–45,992,639 | 262.8 kb | Distal (>10kb) Multiome | 1242 |
Genomic view of the LINC00938 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.