The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP contains an N-terminal domain that shares a significant similarity with yeast SEC14, which is a protein that has phosphatidylinositol transfer activity and is required for protein secretion through the Golgi complex in yeast. This PTP was found to be activated by polyphosphoinositide, and is thought to be involved in signaling events regulating phagocytosis. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PTPN9. 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 = PTPN9 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 PTPN9, 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 |
|---|---|---|---|---|
| chr15:75,335,855–75,336,339 | 243.3 kb | Distal (>10kb) Multiome | 665 | |
| chr15:75,346,877–75,348,733 | 231.9 kb | Distal (>10kb) Multiome | 738 | |
| chr15:75,367,625–75,369,002 | 211.2 kb | Distal (>10kb) Multiome | 1121 | |
| chr15:75,450,273–75,456,388 | 123.4 kb | Distal (>10kb) Multiome | 1174 | |
| chr15:75,578,469–75,578,937 | 377 bp | At TSS | 465 | |
| chr15:75,579,138–75,580,015 | 181 bp | At TSS Multiome | 683 | |
| chr15:75,624,816–75,626,356 | 46.4 kb | Distal (>10kb) Multiome | 987 | |
| chr15:75,639,562–75,640,798 | 61.0 kb | Distal (>10kb) Multiome | 999 | |
| chr15:75,647,017–75,648,674 | 68.5 kb | Distal (>10kb) Multiome | 795 | |
| chr15:75,672,794–75,673,400 | 93.7 kb | Distal (>10kb) Multiome | 226 | |
| chr15:75,712,716–75,713,248 | 133.6 kb | Distal (>10kb) Multiome | 318 | |
| chr15:75,738,177–75,739,332 | 159.4 kb | Distal (>10kb) Multiome | 611 | |
| chr15:75,758,383–75,758,865 | 179.2 kb | Distal (>10kb) Multiome | 550 | |
| chr15:75,823,901–75,824,543 | 244.8 kb | Distal (>10kb) Multiome | 98 | |
| chr15:75,842,738–75,844,503 | 263.9 kb | Distal (>10kb) Multiome | 842 |
Genomic view of the PTPN9 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.