Pyridoxal 5-prime-phosphate (PLP) is the active form of vitamin B6 that acts as a coenzyme in maintaining biochemical homeostasis. The preferred degradation route from PLP to 4-pyridoxic acid involves the dephosphorylation of PLP by PDXP (Jang et al., 2003 [PubMed 14522954]).[supplied by OMIM, Mar 2008]
Transcription factors with Perturb-seq knockdown data for PDXP. 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 = PDXP 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 PDXP, 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 |
|---|---|---|---|---|
| chr22:37,419,824–37,420,580 | 238.5 kb | Distal (>10kb) Multiome | 150 | |
| chr22:37,518,831–37,519,884 | 139.2 kb | Distal (>10kb) Multiome | 548 | |
| chr22:37,545,569–37,546,885 | 112.4 kb | Distal (>10kb) Multiome | 682 | |
| chr22:37,559,893–37,560,965 | 98.4 kb | Distal (>10kb) Multiome | 589 | |
| chr22:37,569,013–37,570,549 | 89.2 kb | Distal (>10kb) Multiome | 695 | |
| chr22:37,608,044–37,609,455 | 49.9 kb | Distal (>10kb) Multiome | 920 | |
| chr22:37,639,157–37,639,951 | 19.2 kb | Distal (>10kb) Multiome | 427 | |
| chr22:37,658,172–37,659,508 | 140 bp | At TSS Multiome | 722 | |
| chr22:37,674,916–37,675,641 | 16.7 kb | Distal (>10kb) Multiome | 607 | |
| chr22:37,676,590–37,677,674 | 18.5 kb | Distal (>10kb) Multiome | 655 | |
| chr22:37,686,104–37,686,784 | 27.7 kb | Distal (>10kb) Multiome | 866 | |
| chr22:37,696,496–37,697,685 | 38.2 kb | Distal (>10kb) Multiome | 428 | |
| chr22:37,745,641–37,746,995 | 87.4 kb | Distal (>10kb) Multiome | 627 | |
| chr22:37,802,124–37,802,989 | 143.7 kb | Distal (>10kb) Multiome | 603 | |
| chr22:37,804,679–37,805,768 | 146.5 kb | Distal (>10kb) Multiome | 763 | |
| chr22:37,807,436–37,808,267 | 149.1 kb | Distal (>10kb) Multiome | 766 | |
| chr22:37,817,672–37,819,114 | 159.2 kb | Distal (>10kb) Multiome | 713 | |
| chr22:37,824,524–37,825,593 | 166.2 kb | Distal (>10kb) Multiome | 173 | |
| chr22:37,843,748–37,844,743 | 185.7 kb | Distal (>10kb) Multiome | 798 | |
| chr22:37,849,215–37,849,709 | 190.7 kb | Distal (>10kb) Multiome | 753 | |
| chr22:37,905,849–37,906,846 | 247.5 kb | Distal (>10kb) Multiome | 552 | |
| chr22:37,933,777–37,934,256 | 275.4 kb | Distal (>10kb) Multiome | 679 | |
| chr22:37,953,153–37,954,120 | 294.9 kb | Distal (>10kb) Multiome | 617 |
Genomic view of the PDXP 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.