Transcription factors with Perturb-seq knockdown data for LINC03053. 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 = LINC03053 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 LINC03053, 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 |
|---|---|---|---|---|
| chrX:40,004,276–40,004,537 | 4.7 kb | Proximal (<10kb) | 59 | |
| chrX:40,006,171–40,006,496 | 2.8 kb | Proximal (<10kb) | 124 | |
| chrX:40,008,825–40,009,356 | at TSS | At TSS | 152 | |
| chrX:40,013,660–40,014,163 | 4.4 kb | Proximal (<10kb) | 456 | |
| chrX:40,014,248–40,015,286 | 5.0 kb | Proximal (<10kb) | 617 |
Genomic view of the LINC03053 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.