Transcription factors with Perturb-seq knockdown data for LINC01004. 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 = LINC01004 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 LINC01004, 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 |
|---|---|---|---|---|
| chr7:104,772,342–104,772,964 | 240.5 kb | Distal (>10kb) Multiome | 138 | |
| chr7:104,883,531–104,884,202 | 129.1 kb | Distal (>10kb) Multiome | 666 | |
| chr7:104,926,844–104,927,636 | 85.8 kb | Distal (>10kb) Multiome | 103 | |
| chr7:104,944,876–104,945,547 | 67.8 kb | Distal (>10kb) Multiome | 743 | |
| chr7:104,979,070–104,979,804 | 33.7 kb | Distal (>10kb) Multiome | 356 | |
| chr7:104,983,612–104,984,567 | 28.9 kb | Distal (>10kb) Multiome | 983 | |
| chr7:105,012,362–105,015,535 | 124 bp | At TSS Multiome | 1271 | |
| chr7:105,015,632–105,015,772 | 2.6 kb | Proximal (<10kb) | 186 |
Genomic view of the LINC01004 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.