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Gene: PTPN4 |
Gene summary for PTPN4 |
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Gene information | Species | Human | Gene symbol | PTPN4 | Gene ID | 5775 |
Gene name | protein tyrosine phosphatase non-receptor type 4 | |
Gene Alias | MEG | |
Cytomap | 2q14.2 | |
Gene Type | protein-coding | GO ID | GO:0006464 | UniProtAcc | A0A024RAE8 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
5775 | PTPN4 | CA_HPV_3 | Human | Cervix | CC | 8.98e-03 | 9.01e-02 | 0.0414 |
5775 | PTPN4 | CCI_3 | Human | Cervix | CC | 1.14e-11 | 7.01e-01 | 0.516 |
5775 | PTPN4 | HTA11_3410_2000001011 | Human | Colorectum | AD | 5.32e-17 | -6.25e-01 | 0.0155 |
5775 | PTPN4 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.31e-04 | -5.43e-01 | -0.1207 |
5775 | PTPN4 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.52e-12 | -5.02e-01 | -0.1464 |
5775 | PTPN4 | HTA11_866_2000001011 | Human | Colorectum | AD | 7.57e-04 | -3.47e-01 | -0.1001 |
5775 | PTPN4 | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.65e-03 | -6.89e-01 | -0.2061 |
5775 | PTPN4 | HTA11_546_2000001011 | Human | Colorectum | AD | 2.81e-02 | -4.99e-01 | -0.0842 |
5775 | PTPN4 | HTA11_866_3004761011 | Human | Colorectum | AD | 7.02e-11 | -5.66e-01 | 0.096 |
5775 | PTPN4 | HTA11_7696_3000711011 | Human | Colorectum | AD | 4.33e-05 | -4.18e-01 | 0.0674 |
5775 | PTPN4 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.24e-07 | -4.48e-01 | 0.294 |
5775 | PTPN4 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.59e-02 | -5.20e-01 | 0.2585 |
5775 | PTPN4 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.16e-05 | -3.52e-01 | 0.3005 |
5775 | PTPN4 | A001-C-207 | Human | Colorectum | FAP | 1.32e-02 | -2.27e-01 | 0.1278 |
5775 | PTPN4 | A015-C-203 | Human | Colorectum | FAP | 1.59e-26 | -2.97e-01 | -0.1294 |
5775 | PTPN4 | A015-C-204 | Human | Colorectum | FAP | 2.98e-04 | -2.45e-01 | -0.0228 |
5775 | PTPN4 | A014-C-040 | Human | Colorectum | FAP | 1.42e-03 | -3.98e-01 | -0.1184 |
5775 | PTPN4 | A002-C-201 | Human | Colorectum | FAP | 2.25e-12 | -1.62e-01 | 0.0324 |
5775 | PTPN4 | A002-C-203 | Human | Colorectum | FAP | 4.57e-02 | -1.33e-01 | 0.2786 |
5775 | PTPN4 | A001-C-119 | Human | Colorectum | FAP | 4.11e-05 | -2.94e-01 | -0.1557 |
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∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
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Tissue | Disease Stage | Enriched GO biological Processes |
Colorectum | AD | ![]() |
Colorectum | SER | ![]() |
Colorectum | MSS | ![]() |
Colorectum | MSI-H | ![]() |
Colorectum | FAP | ![]() |
∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
Page: 1 2 3 4 5 6 7 8 9 |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00064708 | Cervix | CC | protein dephosphorylation | 60/2311 | 281/18723 | 1.33e-05 | 2.68e-04 | 60 |
GO:00163117 | Cervix | CC | dephosphorylation | 73/2311 | 417/18723 | 1.23e-03 | 9.87e-03 | 73 |
GO:0016311 | Colorectum | AD | dephosphorylation | 123/3918 | 417/18723 | 1.84e-05 | 3.82e-04 | 123 |
GO:0006470 | Colorectum | AD | protein dephosphorylation | 88/3918 | 281/18723 | 2.56e-05 | 4.89e-04 | 88 |
GO:00064702 | Colorectum | MSS | protein dephosphorylation | 73/3467 | 281/18723 | 1.15e-03 | 1.12e-02 | 73 |
GO:00163112 | Colorectum | MSS | dephosphorylation | 101/3467 | 417/18723 | 1.98e-03 | 1.70e-02 | 101 |
GO:00163113 | Colorectum | FAP | dephosphorylation | 95/2622 | 417/18723 | 7.07e-07 | 3.32e-05 | 95 |
GO:00064704 | Colorectum | FAP | protein dephosphorylation | 69/2622 | 281/18723 | 1.47e-06 | 6.39e-05 | 69 |
GO:0035335 | Colorectum | FAP | peptidyl-tyrosine dephosphorylation | 23/2622 | 97/18723 | 6.95e-03 | 4.26e-02 | 23 |
GO:00163114 | Colorectum | CRC | dephosphorylation | 79/2078 | 417/18723 | 1.27e-06 | 7.21e-05 | 79 |
GO:00064705 | Colorectum | CRC | protein dephosphorylation | 57/2078 | 281/18723 | 4.49e-06 | 1.87e-04 | 57 |
GO:00064709 | Endometrium | AEH | protein dephosphorylation | 50/2100 | 281/18723 | 6.41e-04 | 6.23e-03 | 50 |
GO:000647013 | Endometrium | EEC | protein dephosphorylation | 51/2168 | 281/18723 | 7.38e-04 | 7.01e-03 | 51 |
GO:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
GO:000647018 | Esophagus | ESCC | protein dephosphorylation | 177/8552 | 281/18723 | 3.13e-09 | 6.72e-08 | 177 |
GO:00163115 | Liver | NAFLD | dephosphorylation | 69/1882 | 417/18723 | 2.27e-05 | 6.23e-04 | 69 |
GO:00064706 | Liver | NAFLD | protein dephosphorylation | 50/1882 | 281/18723 | 4.53e-05 | 1.09e-03 | 50 |
GO:000647011 | Liver | Cirrhotic | protein dephosphorylation | 96/4634 | 281/18723 | 2.32e-04 | 2.11e-03 | 96 |
GO:001631111 | Liver | Cirrhotic | dephosphorylation | 130/4634 | 417/18723 | 1.58e-03 | 1.03e-02 | 130 |
GO:001631121 | Liver | HCC | dephosphorylation | 230/7958 | 417/18723 | 1.00e-07 | 1.96e-06 | 230 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
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Somatic mutation of malignant transformation related genes |
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Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
PTPN4 | SNV | Missense_Mutation | rs781516454 | c.1168N>C | p.Ser390Pro | p.S390P | P29074 | protein_coding | deleterious(0.02) | benign(0.135) | TCGA-94-8491-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | unknown | PD |
PTPN4 | insertion | Frame_Shift_Ins | novel | c.2031_2032insAA | p.Gln678AsnfsTer22 | p.Q678Nfs*22 | P29074 | protein_coding | TCGA-44-4112-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Chemotherapy | cisplatin | PD | ||
PTPN4 | deletion | Frame_Shift_Del | novel | c.2151delC | p.Ser718AlafsTer3 | p.S718Afs*3 | P29074 | protein_coding | TCGA-55-A4DG-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
PTPN4 | insertion | Nonsense_Mutation | novel | c.2166_2168dupGTA | p.Gln722_Tyr723insTer | p.Q722_Y723ins* | P29074 | protein_coding | TCGA-62-A472-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | ||
PTPN4 | deletion | Frame_Shift_Del | novel | c.443delN | p.Leu149Ter | p.L149* | P29074 | protein_coding | TCGA-63-A5MS-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
PTPN4 | deletion | Frame_Shift_Del | novel | c.1902delN | p.Asp635MetfsTer9 | p.D635Mfs*9 | P29074 | protein_coding | TCGA-66-2759-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Chemotherapy | carboplatin | CR | ||
PTPN4 | SNV | Missense_Mutation | novel | c.2153N>T | p.Ser718Ile | p.S718I | P29074 | protein_coding | deleterious(0) | benign(0.077) | TCGA-BA-5555-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
PTPN4 | SNV | Missense_Mutation | novel | c.1900N>G | p.Gln634Glu | p.Q634E | P29074 | protein_coding | tolerated(1) | benign(0.007) | TCGA-CN-4738-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
PTPN4 | SNV | Missense_Mutation | novel | c.1939G>T | p.Ala647Ser | p.A647S | P29074 | protein_coding | tolerated(0.36) | benign(0) | TCGA-CV-5430-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | carboplatin | PD |
PTPN4 | SNV | Missense_Mutation | novel | c.145N>T | p.Asp49Tyr | p.D49Y | P29074 | protein_coding | deleterious(0.01) | benign(0.192) | TCGA-CV-A45W-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
5775 | PTPN4 | PROTEIN PHOSPHATASE, DRUGGABLE GENOME | ALENDRONATE | ALENDRONIC ACID |
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