Transcription factors with Perturb-seq knockdown data for TMA7. 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 = TMA7 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 TMA7, 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 |
|---|---|---|---|---|
| chr3:48,187,500–48,188,989 | 251.7 kb | Distal (>10kb) Multiome | 820 | |
| chr3:48,240,728–48,241,473 | 199.1 kb | Distal (>10kb) Multiome HiCAR | 843 | |
| chr3:48,300,947–48,301,746 | 138.8 kb | Distal (>10kb) Multiome | 954 | |
| chr3:48,372,864–48,373,543 | 67.0 kb | Distal (>10kb) Multiome | 49 | |
| chr3:48,428,528–48,430,504 | 10.2 kb | Distal (>10kb) Multiome | 910 | |
| chr3:48,432,876–48,433,064 | 7.2 kb | Proximal (<10kb) | 68 | |
| chr3:48,435,863–48,436,304 | 4.0 kb | Proximal (<10kb) | 452 | |
| chr3:48,439,801–48,440,548 | 78 bp | At TSS Multiome | 787 | |
| chr3:48,446,396–48,447,180 | 6.5 kb | Proximal (<10kb) Multiome | 767 | |
| chr3:48,465,344–48,466,310 | 25.5 kb | Distal (>10kb) Multiome | 670 | |
| chr3:48,472,636–48,473,658 | 33.0 kb | Distal (>10kb) Multiome | 821 | |
| chr3:48,503,451–48,504,839 | 63.9 kb | Distal (>10kb) Multiome | 419 | |
| chr3:48,556,022–48,557,666 | 116.8 kb | Distal (>10kb) Multiome | 794 | |
| chr3:48,558,131–48,558,793 | 118.2 kb | Distal (>10kb) Multiome | 503 | |
| chr3:48,608,816–48,610,628 | 169.4 kb | Distal (>10kb) Multiome | 850 | |
| chr3:48,634,696–48,636,251 | 195.3 kb | Distal (>10kb) Multiome | 898 | |
| chr3:48,655,787–48,657,257 | 216.2 kb | Distal (>10kb) Multiome | 438 | |
| chr3:48,661,275–48,664,636 | 221.5 kb | Distal (>10kb) Multiome | 1248 | |
| chr3:48,685,362–48,686,531 | 245.6 kb | Distal (>10kb) Multiome | 770 | |
| chr3:48,716,958–48,717,863 | 277.1 kb | Distal (>10kb) Multiome | 634 |
Genomic view of the TMA7 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.