LIN54 is a component of the LIN, or DREAM, complex, an essential regulator of cell cycle genes (Schmit et al., 2009 [PubMed 19725879]).[supplied by OMIM, Dec 2010]
Transcription factors with Perturb-seq knockdown data for LIN54. 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 = LIN54 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 LIN54, 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 |
|---|---|---|---|---|
| chr4:82,716,050–82,716,644 | 296.5 kb | Distal (>10kb) Multiome | 173 | |
| chr4:82,739,190–82,739,774 | 273.4 kb | Distal (>10kb) Multiome | 317 | |
| chr4:82,797,244–82,798,074 | 215.5 kb | Distal (>10kb) Multiome | 243 | |
| chr4:82,798,169–82,799,103 | 214.1 kb | Distal (>10kb) Multiome | 368 | |
| chr4:82,890,719–82,891,825 | 121.7 kb | Distal (>10kb) Multiome | 1005 | |
| chr4:82,899,856–82,901,464 | 112.2 kb | Distal (>10kb) Multiome | 977 | |
| chr4:83,010,137–83,011,179 | 2.2 kb | Proximal (<10kb) Multiome | 601 | |
| chr4:83,012,161–83,013,775 | 125 bp | At TSS Multiome | 913 | |
| chr4:83,034,341–83,035,668 | 22.1 kb | Distal (>10kb) Multiome | 993 | |
| chr4:83,109,433–83,110,778 | 96.8 kb | Distal (>10kb) Multiome | 591 | |
| chr4:83,283,973–83,285,305 | 271.7 kb | Distal (>10kb) Multiome | 879 |
Genomic view of the LIN54 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.