Ephrin receptors and their ligands, the ephrins, mediate numerous developmental processes, particularly in the nervous system. Based on their structures and sequence relationships, ephrins are divided into the ephrin-A (EFNA) class, which are anchored to the membrane by a glycosylphosphatidylinositol linkage, and the ephrin-B (EFNB) class, which are transmembrane proteins. The Eph family of receptors are divided into 2 groups based on the similarity of their extracellular domain sequences and their affinities for binding ephrin-A and ephrin-B ligands. Ephrin receptors make up the largest subgroup of the receptor tyrosine kinase (RTK) family. The protein encoded by this gene binds to ephrin-B2 and plays an essential role in vascular development. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for EPHB4. 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 = EPHB4 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 EPHB4, 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 |
|---|---|---|---|---|
| chr7:100,482,937–100,484,533 | 343.9 kb | Distal (>10kb) Multiome HiCAR | 677 | |
| chr7:100,538,557–100,539,759 | 288.5 kb | Distal (>10kb) Multiome | 858 | |
| chr7:100,542,221–100,542,986 | 284.8 kb | Distal (>10kb) Multiome | 274 | |
| chr7:100,569,177–100,570,642 | 257.9 kb | Distal (>10kb) Multiome | 855 | |
| chr7:100,585,161–100,587,241 | 241.1 kb | Distal (>10kb) Multiome | 966 | |
| chr7:100,611,685–100,612,981 | 215.3 kb | Distal (>10kb) Multiome | 767 | |
| chr7:100,626,427–100,627,057 | 200.8 kb | Distal (>10kb) Multiome | 415 | |
| chr7:100,656,111–100,656,626 | 171.1 kb | Distal (>10kb) Multiome | 653 | |
| chr7:100,673,043–100,674,892 | 154.0 kb | Distal (>10kb) Multiome | 934 | |
| chr7:100,674,996–100,676,406 | 151.6 kb | Distal (>10kb) Multiome | 439 | |
| chr7:100,691,570–100,692,163 | 135.6 kb | Distal (>10kb) Multiome HiCAR | 364 | |
| chr7:100,693,475–100,694,667 | 133.2 kb | Distal (>10kb) Multiome HiCAR | 607 | |
| chr7:100,705,140–100,706,426 | 121.6 kb | Distal (>10kb) Multiome | 962 | |
| chr7:100,827,001–100,828,324 | 138 bp | At TSS Multiome | 794 | |
| chr7:100,828,481–100,828,942 | 1.4 kb | Proximal (<10kb) | 250 | |
| chr7:100,835,906–100,837,766 | 9.3 kb | Proximal (<10kb) Multiome | 766 | |
| chr7:100,852,057–100,853,190 | 25.0 kb | Distal (>10kb) Multiome | 805 | |
| chr7:100,874,652–100,875,664 | 47.5 kb | Distal (>10kb) Multiome | 1020 | |
| chr7:100,888,882–100,891,520 | 62.3 kb | Distal (>10kb) Multiome | 1077 | |
| chr7:100,894,188–100,896,392 | 68.5 kb | Distal (>10kb) Multiome | 609 | |
| chr7:100,896,481–100,897,567 | 69.6 kb | Distal (>10kb) Multiome | 538 | |
| chr7:101,085,076–101,085,958 | 258.0 kb | Distal (>10kb) Multiome | 732 |
Genomic view of the EPHB4 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.