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Gene: PTPN2 |
Gene summary for PTPN2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTPN2 | Gene ID | 5771 |
| Gene name | protein tyrosine phosphatase non-receptor type 2 | |
| Gene Alias | PTN2 | |
| Cytomap | 18p11.21 | |
| Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | P17706 |
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Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 5771 | PTPN2 | CA_HPV_1 | Human | Cervix | CC | 3.73e-02 | 1.63e-01 | 0.0264 |
| 5771 | PTPN2 | CCI_1 | Human | Cervix | CC | 9.44e-03 | 6.25e-01 | 0.528 |
| 5771 | PTPN2 | CCI_3 | Human | Cervix | CC | 1.55e-02 | 5.66e-01 | 0.516 |
| 5771 | PTPN2 | LZE2D | Human | Esophagus | HGIN | 1.02e-02 | 2.93e-01 | 0.0642 |
| 5771 | PTPN2 | LZE3D | Human | Esophagus | HGIN | 1.23e-02 | 8.78e-01 | 0.0668 |
| 5771 | PTPN2 | LZE4T | Human | Esophagus | ESCC | 1.79e-11 | 3.85e-01 | 0.0811 |
| 5771 | PTPN2 | LZE5T | Human | Esophagus | ESCC | 2.36e-02 | 4.60e-01 | 0.0514 |
| 5771 | PTPN2 | LZE7T | Human | Esophagus | ESCC | 1.70e-08 | 7.10e-01 | 0.0667 |
| 5771 | PTPN2 | LZE8T | Human | Esophagus | ESCC | 1.57e-08 | 3.58e-01 | 0.067 |
| 5771 | PTPN2 | LZE20T | Human | Esophagus | ESCC | 9.63e-08 | 2.16e-01 | 0.0662 |
| 5771 | PTPN2 | LZE22D1 | Human | Esophagus | HGIN | 1.37e-02 | 1.68e-01 | 0.0595 |
| 5771 | PTPN2 | LZE22T | Human | Esophagus | ESCC | 1.76e-03 | 7.01e-01 | 0.068 |
| 5771 | PTPN2 | LZE24T | Human | Esophagus | ESCC | 3.56e-24 | 8.39e-01 | 0.0596 |
| 5771 | PTPN2 | LZE21T | Human | Esophagus | ESCC | 1.18e-09 | 7.07e-01 | 0.0655 |
| 5771 | PTPN2 | P1T-E | Human | Esophagus | ESCC | 8.38e-08 | 7.06e-01 | 0.0875 |
| 5771 | PTPN2 | P2T-E | Human | Esophagus | ESCC | 7.05e-45 | 1.06e+00 | 0.1177 |
| 5771 | PTPN2 | P4T-E | Human | Esophagus | ESCC | 1.01e-35 | 9.74e-01 | 0.1323 |
| 5771 | PTPN2 | P5T-E | Human | Esophagus | ESCC | 3.79e-53 | 1.19e+00 | 0.1327 |
| 5771 | PTPN2 | P8T-E | Human | Esophagus | ESCC | 7.97e-36 | 7.79e-01 | 0.0889 |
| 5771 | PTPN2 | P9T-E | Human | Esophagus | ESCC | 5.37e-25 | 8.11e-01 | 0.1131 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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 |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| 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 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0033673110 | Skin | cSCC | negative regulation of kinase activity | 81/4864 | 237/18723 | 2.95e-03 | 1.64e-02 | 81 |
| GO:190118510 | Skin | cSCC | negative regulation of ERBB signaling pathway | 16/4864 | 32/18723 | 3.04e-03 | 1.67e-02 | 16 |
| GO:004508812 | Skin | cSCC | regulation of innate immune response | 75/4864 | 218/18723 | 3.40e-03 | 1.84e-02 | 75 |
| GO:004800822 | Skin | cSCC | platelet-derived growth factor receptor signaling pathway | 24/4864 | 56/18723 | 4.44e-03 | 2.29e-02 | 24 |
| GO:00507323 | Skin | cSCC | negative regulation of peptidyl-tyrosine phosphorylation | 25/4864 | 59/18723 | 4.46e-03 | 2.29e-02 | 25 |
| GO:00706706 | Skin | cSCC | response to interleukin-4 | 17/4864 | 36/18723 | 4.85e-03 | 2.46e-02 | 17 |
| GO:005123527 | Skin | cSCC | maintenance of location | 106/4864 | 327/18723 | 5.17e-03 | 2.61e-02 | 106 |
| GO:190210524 | Skin | cSCC | regulation of leukocyte differentiation | 92/4864 | 279/18723 | 5.20e-03 | 2.63e-02 | 92 |
| GO:00603393 | Skin | cSCC | negative regulation of type I interferon-mediated signaling pathway | 11/4864 | 20/18723 | 5.40e-03 | 2.71e-02 | 11 |
| GO:000828616 | Skin | cSCC | insulin receptor signaling pathway | 43/4864 | 116/18723 | 5.44e-03 | 2.73e-02 | 43 |
| GO:00607596 | Skin | cSCC | regulation of response to cytokine stimulus | 57/4864 | 162/18723 | 5.77e-03 | 2.85e-02 | 57 |
| GO:000599610 | Skin | cSCC | monosaccharide metabolic process | 85/4864 | 257/18723 | 6.43e-03 | 3.14e-02 | 85 |
| GO:004801211 | Skin | cSCC | hepatocyte growth factor receptor signaling pathway | 8/4864 | 13/18723 | 7.25e-03 | 3.44e-02 | 8 |
| GO:000716224 | Skin | cSCC | negative regulation of cell adhesion | 98/4864 | 303/18723 | 7.45e-03 | 3.50e-02 | 98 |
| GO:004562021 | Skin | cSCC | negative regulation of lymphocyte differentiation | 23/4864 | 55/18723 | 7.54e-03 | 3.53e-02 | 23 |
| GO:00458246 | Skin | cSCC | negative regulation of innate immune response | 28/4864 | 71/18723 | 8.86e-03 | 4.07e-02 | 28 |
| GO:000600610 | Skin | cSCC | glucose metabolic process | 66/4864 | 196/18723 | 9.75e-03 | 4.32e-02 | 66 |
| GO:005085221 | Skin | cSCC | T cell receptor signaling pathway | 44/4864 | 123/18723 | 1.02e-02 | 4.47e-02 | 44 |
| GO:000276123 | Skin | cSCC | regulation of myeloid leukocyte differentiation | 43/4864 | 120/18723 | 1.06e-02 | 4.66e-02 | 43 |
| GO:0034976113 | Thyroid | PTC | response to endoplasmic reticulum stress | 161/5968 | 256/18723 | 1.14e-24 | 3.27e-22 | 161 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04630 | Oral cavity | EOLP | JAK-STAT signaling pathway | 35/1218 | 166/8465 | 1.15e-02 | 3.07e-02 | 1.81e-02 | 35 |
| hsa046301 | Oral cavity | EOLP | JAK-STAT signaling pathway | 35/1218 | 166/8465 | 1.15e-02 | 3.07e-02 | 1.81e-02 | 35 |
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Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
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Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| 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. |
| Page: 1 |
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Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| 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 |
| PTPN2 | SNV | Missense_Mutation | c.193G>C | p.Glu65Gln | p.E65Q | P17706 | protein_coding | tolerated(0.11) | benign(0.153) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PTPN2 | SNV | Missense_Mutation | c.491T>G | p.Ile164Ser | p.I164S | P17706 | protein_coding | deleterious(0.03) | benign(0.143) | TCGA-C8-A12L-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PTPN2 | SNV | Missense_Mutation | rs779158537 | c.1054N>T | p.Arg352Cys | p.R352C | P17706 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PTPN2 | SNV | Missense_Mutation | c.312N>C | p.Gln104His | p.Q104H | P17706 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD | |
| PTPN2 | SNV | Missense_Mutation | novel | c.890N>C | p.Leu297Ser | p.L297S | P17706 | protein_coding | tolerated(0.25) | benign(0.137) | TCGA-DS-A1OD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| PTPN2 | SNV | Missense_Mutation | c.49C>T | p.Arg17Cys | p.R17C | P17706 | protein_coding | tolerated(0.05) | benign(0.003) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PTPN2 | insertion | Frame_Shift_Ins | novel | c.891_892insCTGT | p.Ser298LeufsTer6 | p.S298Lfs*6 | P17706 | protein_coding | TCGA-DS-A1OD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | ||
| PTPN2 | deletion | Frame_Shift_Del | novel | c.922_925delATAA | p.Ile308Ter | p.I308* | P17706 | protein_coding | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
| PTPN2 | SNV | Missense_Mutation | novel | c.139N>G | p.Arg47Gly | p.R47G | P17706 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| PTPN2 | SNV | Missense_Mutation | c.242N>C | p.Arg81Thr | p.R81T | P17706 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AA-3930-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | capecitabine | PD |
| Page: 1 2 3 4 5 |
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Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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