Gene Page: PTPN3
Summary ?
| GeneID | 5774 |
| Symbol | PTPN3 |
| Synonyms | PTP-H1|PTPH1 |
| Description | protein tyrosine phosphatase, non-receptor type 3 |
| Reference | MIM:176877|HGNC:HGNC:9655|Ensembl:ENSG00000070159|HPRD:06767|Vega:OTTHUMG00000020475 |
| Gene type | protein-coding |
| Map location | 9q31 |
| Pascal p-value | 0.023 |
| Fetal beta | -2.333 |
| eGene | Myers' cis & trans |
| Support | CompositeSet Ascano FMRP targets |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DNM:Fromer_2014 | Whole Exome Sequencing analysis | This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA. |
Section I. Genetics and epigenetics annotation
DNM table
| Gene | Chromosome | Position | Ref | Alt | Transcript | AA change | Mutation type | Sift | CG46 | Trait | Study |
|---|---|---|---|---|---|---|---|---|---|---|---|
| PTPN3 | chr9 | 112172670 | G | T | NM_001145368 NM_001145369 NM_001145370 NM_001145371 NM_001145372 NM_002829 NR_026918 | p.402Q>K p.316Q>K p.271Q>K p.160Q>K p.115Q>K p.447Q>K . | missense missense missense missense missense missense npcRNA | Schizophrenia | DNM:Fromer_2014 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs17186508 | chr5 | 65194022 | PTPN3 | 5774 | 0.05 | trans | ||
| rs1030841 | chr10 | 34812290 | PTPN3 | 5774 | 0.11 | trans | ||
| rs6021571 | chr20 | 50574626 | PTPN3 | 5774 | 0.19 | trans |
Section II. Transcriptome annotation
General gene expression (GTEx)
Gene expression during devlopment (BrainCloud)
Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.
Gene expression of temporal and spatial changes (BrainSpan)
Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.
Top co-expressed genes in brain regions
| Top 10 positively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| ZNF193 | 0.86 | 0.80 |
| NUP93 | 0.83 | 0.89 |
| ZNF608 | 0.82 | 0.83 |
| C19orf57 | 0.81 | 0.85 |
| SEMA6C | 0.80 | 0.86 |
| GTF2IRD2B | 0.80 | 0.79 |
| LOXL3 | 0.80 | 0.78 |
| ZNF435 | 0.80 | 0.76 |
| DNAJC9 | 0.80 | 0.88 |
| HES6 | 0.79 | 0.69 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| HLA-F | -0.61 | -0.74 |
| AIFM3 | -0.60 | -0.71 |
| FBXO2 | -0.59 | -0.62 |
| C5orf53 | -0.59 | -0.69 |
| ALDOC | -0.59 | -0.67 |
| PTH1R | -0.58 | -0.67 |
| LDHD | -0.58 | -0.63 |
| CA4 | -0.57 | -0.67 |
| ZNF385A | -0.57 | -0.68 |
| S100B | -0.57 | -0.76 |
Section V. Pathway annotation
| Pathway name | Pathway size | # SZGR 2.0 genes in pathway | Info |
|---|---|---|---|
| AKL HTLV1 INFECTION DN | 68 | 41 | All SZGR 2.0 genes in this pathway |
| DODD NASOPHARYNGEAL CARCINOMA UP | 1821 | 933 | All SZGR 2.0 genes in this pathway |
| GAUSSMANN MLL AF4 FUSION TARGETS G UP | 238 | 135 | All SZGR 2.0 genes in this pathway |
| LINDGREN BLADDER CANCER WITH LOH IN CHR9Q | 116 | 71 | All SZGR 2.0 genes in this pathway |
| HERNANDEZ ABERRANT MITOSIS BY DOCETACEL 2NM UP | 81 | 57 | All SZGR 2.0 genes in this pathway |
| BENPORATH SOX2 TARGETS | 734 | 436 | All SZGR 2.0 genes in this pathway |
| ONDER CDH1 TARGETS 2 DN | 464 | 276 | All SZGR 2.0 genes in this pathway |
| FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN | 546 | 351 | All SZGR 2.0 genes in this pathway |
| TAVOR CEBPA TARGETS UP | 48 | 36 | All SZGR 2.0 genes in this pathway |
| KAAB HEART ATRIUM VS VENTRICLE DN | 261 | 183 | All SZGR 2.0 genes in this pathway |
| BROWNE HCMV INFECTION 18HR UP | 178 | 111 | All SZGR 2.0 genes in this pathway |
| DAZARD RESPONSE TO UV NHEK DN | 318 | 220 | All SZGR 2.0 genes in this pathway |
| XU GH1 AUTOCRINE TARGETS DN | 142 | 94 | All SZGR 2.0 genes in this pathway |
| BANDRES RESPONSE TO CARMUSTIN MGMT 48HR DN | 161 | 105 | All SZGR 2.0 genes in this pathway |
| CREIGHTON ENDOCRINE THERAPY RESISTANCE 3 | 720 | 440 | All SZGR 2.0 genes in this pathway |
| ACEVEDO METHYLATED IN LIVER CANCER DN | 940 | 425 | All SZGR 2.0 genes in this pathway |
| TOYOTA TARGETS OF MIR34B AND MIR34C | 463 | 262 | All SZGR 2.0 genes in this pathway |
| BONCI TARGETS OF MIR15A AND MIR16 1 | 91 | 75 | All SZGR 2.0 genes in this pathway |
| MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 | 1069 | 729 | All SZGR 2.0 genes in this pathway |
| GABRIELY MIR21 TARGETS | 289 | 187 | All SZGR 2.0 genes in this pathway |
| TORCHIA TARGETS OF EWSR1 FLI1 FUSION DN | 321 | 200 | All SZGR 2.0 genes in this pathway |
| BOSCO EPITHELIAL DIFFERENTIATION MODULE | 69 | 31 | All SZGR 2.0 genes in this pathway |