Transcription factors with Perturb-seq knockdown data for LINC01088. 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 = LINC01088 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 LINC01088, 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 |
|---|---|---|---|---|
| chr4:78,775,275–78,777,335 | 163.3 kb | Distal (>10kb) Multiome | 938 | |
| chr4:78,938,845–78,940,140 | 80 bp | At TSS Multiome | 723 | |
| chr4:80,183,397–80,184,999 | 1244.7 kb | Distal (>10kb) Multiome HiCAR | 610 | |
| chr4:80,189,905–80,190,753 | 1250.8 kb | Distal (>10kb) Multiome HiCAR | 185 | |
| chr4:80,196,927–80,198,313 | 1258.3 kb | Distal (>10kb) Multiome HiCAR | 272 | |
| chr4:80,265,601–80,267,391 | 1327.3 kb | Distal (>10kb) Multiome HiCAR | 474 |
Genomic view of the LINC01088 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.