Transcription factors with Perturb-seq knockdown data for LINC01140. 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 = LINC01140 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 LINC01140, 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 |
|---|---|---|---|---|
| chr1:87,130,510–87,130,879 | 1.1 kb | Proximal (<10kb) | 75 | |
| chr1:87,131,612–87,132,886 | at TSS | At TSS | 494 | |
| chr1:87,133,487–87,134,387 | 1.5 kb | Proximal (<10kb) | 138 | |
| chr1:87,134,621–87,134,921 | 2.7 kb | Proximal (<10kb) | 13 |
Genomic view of the LINC01140 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.