Transcription factors with Perturb-seq knockdown data for LINC01438. 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 = LINC01438 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 LINC01438, 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 |
|---|---|---|---|---|
| chr4:110,790,530–110,790,921 | 3.5 kb | Proximal (<10kb) | 6 | |
| chr4:110,791,713–110,792,349 | 2.1 kb | Proximal (<10kb) | 55 | |
| chr4:110,792,455–110,792,844 | 1.6 kb | Proximal (<10kb) | 13 | |
| chr4:110,793,382–110,794,932 | at TSS | At TSS | 287 |
Genomic view of the LINC01438 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.