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Gene: PTPRN2 |
Gene summary for PTPRN2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PTPRN2 | Gene ID | 5799 |
| Gene name | protein tyrosine phosphatase receptor type N2 | |
| Gene Alias | IA-2beta | |
| Cytomap | 7q36.3 | |
| Gene Type | protein-coding | GO ID | GO:0001505 | UniProtAcc | E7EM83 |
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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 |
| 5799 | PTPRN2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.59e-06 | 5.30e-01 | -0.1808 |
| 5799 | PTPRN2 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.82e-05 | 4.80e-01 | -0.1088 |
| 5799 | PTPRN2 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.07e-07 | 1.87e+00 | -0.2602 |
| 5799 | PTPRN2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 3.25e-02 | 1.15e+00 | -0.2196 |
| 5799 | PTPRN2 | HTA11_696_2000001011 | Human | Colorectum | AD | 2.37e-20 | 7.77e-01 | -0.1464 |
| 5799 | PTPRN2 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.67e-08 | 5.31e-01 | -0.1001 |
| 5799 | PTPRN2 | HTA11_6818_2000001021 | Human | Colorectum | AD | 3.55e-08 | 6.12e-01 | 0.0588 |
| 5799 | PTPRN2 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.90e-09 | 1.74e+00 | 0.3487 |
| 5799 | PTPRN2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 6.29e-09 | 5.55e-01 | 0.281 |
| 5799 | PTPRN2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.07e-06 | 3.32e-01 | 0.3859 |
| 5799 | PTPRN2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.11e-12 | 4.31e-01 | 0.3005 |
| 5799 | PTPRN2 | A015-C-005 | Human | Colorectum | FAP | 1.21e-14 | 7.75e-01 | -0.0336 |
| 5799 | PTPRN2 | A015-C-006 | Human | Colorectum | FAP | 1.12e-19 | 9.12e-01 | -0.0994 |
| 5799 | PTPRN2 | F072B | Human | Colorectum | FAP | 2.34e-02 | 3.84e-01 | 0.257 |
| 5799 | PTPRN2 | CRC-1-8810 | Human | Colorectum | CRC | 4.15e-14 | 5.93e-01 | 0.6257 |
| 5799 | PTPRN2 | CRC-3-11773 | Human | Colorectum | CRC | 4.57e-32 | 8.98e-01 | 0.2564 |
| 5799 | PTPRN2 | HTA12-15-2 | Human | Pancreas | PDAC | 4.30e-05 | 8.49e-01 | 0.2315 |
| 5799 | PTPRN2 | HTA12-23-1 | Human | Pancreas | PDAC | 2.27e-17 | 1.53e+00 | 0.3405 |
| 5799 | PTPRN2 | HTA12-25-1 | Human | Pancreas | PDAC | 1.15e-20 | 1.44e+00 | 0.313 |
| 5799 | PTPRN2 | HTA12-26-1 | Human | Pancreas | PDAC | 1.45e-41 | 1.68e+00 | 0.3728 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal 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:0030072 | Colorectum | AD | peptide hormone secretion | 68/3918 | 236/18723 | 2.39e-03 | 1.85e-02 | 68 |
| GO:0002790 | Colorectum | AD | peptide secretion | 69/3918 | 242/18723 | 2.97e-03 | 2.22e-02 | 69 |
| GO:0042886 | Colorectum | AD | amide transport | 83/3918 | 301/18723 | 3.37e-03 | 2.46e-02 | 83 |
| GO:00342841 | Colorectum | SER | response to monosaccharide | 56/2897 | 225/18723 | 1.52e-04 | 2.98e-03 | 56 |
| GO:00097431 | Colorectum | SER | response to carbohydrate | 60/2897 | 253/18723 | 3.66e-04 | 5.67e-03 | 60 |
| GO:00097491 | Colorectum | SER | response to glucose | 52/2897 | 212/18723 | 3.75e-04 | 5.74e-03 | 52 |
| GO:00064701 | Colorectum | SER | protein dephosphorylation | 65/2897 | 281/18723 | 4.44e-04 | 6.51e-03 | 65 |
| GO:00097461 | Colorectum | SER | response to hexose | 53/2897 | 219/18723 | 4.69e-04 | 6.76e-03 | 53 |
| GO:00430871 | Colorectum | SER | regulation of GTPase activity | 77/2897 | 348/18723 | 5.90e-04 | 8.07e-03 | 77 |
| GO:00093061 | Colorectum | SER | protein secretion | 79/2897 | 359/18723 | 5.99e-04 | 8.19e-03 | 79 |
| GO:00355921 | Colorectum | SER | establishment of protein localization to extracellular region | 79/2897 | 360/18723 | 6.54e-04 | 8.77e-03 | 79 |
| GO:00716921 | Colorectum | SER | protein localization to extracellular region | 80/2897 | 368/18723 | 8.13e-04 | 1.01e-02 | 80 |
| GO:0051346 | Colorectum | SER | negative regulation of hydrolase activity | 82/2897 | 379/18723 | 8.19e-04 | 1.01e-02 | 82 |
| GO:00300731 | Colorectum | SER | insulin secretion | 46/2897 | 195/18723 | 1.86e-03 | 1.90e-02 | 46 |
| GO:00713331 | Colorectum | SER | cellular response to glucose stimulus | 37/2897 | 151/18723 | 2.48e-03 | 2.33e-02 | 37 |
| GO:00163111 | Colorectum | SER | dephosphorylation | 86/2897 | 417/18723 | 2.73e-03 | 2.46e-02 | 86 |
| GO:00425931 | Colorectum | SER | glucose homeostasis | 57/2897 | 258/18723 | 2.92e-03 | 2.59e-02 | 57 |
| GO:00158331 | Colorectum | SER | peptide transport | 58/2897 | 264/18723 | 3.08e-03 | 2.70e-02 | 58 |
| GO:00713311 | Colorectum | SER | cellular response to hexose stimulus | 37/2897 | 153/18723 | 3.15e-03 | 2.73e-02 | 37 |
| GO:00335001 | Colorectum | SER | carbohydrate homeostasis | 57/2897 | 259/18723 | 3.20e-03 | 2.76e-02 | 57 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
| PTPRN2 | SNV | Missense_Mutation | rs748134802 | c.1046N>A | p.Arg349Gln | p.R349Q | Q92932 | protein_coding | tolerated(0.91) | benign(0) | TCGA-5L-AAT0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| PTPRN2 | SNV | Missense_Mutation | c.2518N>A | p.Val840Met | p.V840M | Q92932 | protein_coding | deleterious(0) | possibly_damaging(0.529) | TCGA-AN-A0AL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PTPRN2 | SNV | Missense_Mutation | c.2377N>T | p.Asn793Tyr | p.N793Y | Q92932 | protein_coding | deleterious(0.02) | possibly_damaging(0.862) | TCGA-AR-A255-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | trastuzumab | SD | |
| PTPRN2 | SNV | Missense_Mutation | rs541201905 | c.907N>A | p.Asp303Asn | p.D303N | Q92932 | protein_coding | deleterious(0.04) | benign(0.075) | TCGA-B6-A0X5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| PTPRN2 | SNV | Missense_Mutation | rs551350068 | c.832N>A | p.Pro278Thr | p.P278T | Q92932 | protein_coding | tolerated(0.17) | benign(0.244) | TCGA-D8-A27T-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicine+cyclophosphamide | SD |
| PTPRN2 | SNV | Missense_Mutation | c.2800T>C | p.Tyr934His | p.Y934H | Q92932 | protein_coding | deleterious(0.01) | probably_damaging(0.993) | TCGA-E2-A1LA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | |
| PTPRN2 | SNV | Missense_Mutation | c.1754N>A | p.Ser585Tyr | p.S585Y | Q92932 | protein_coding | deleterious(0) | possibly_damaging(0.808) | TCGA-E9-A1N9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| PTPRN2 | SNV | Missense_Mutation | rs756980461 | c.248N>A | p.Arg83His | p.R83H | Q92932 | protein_coding | deleterious(0.01) | possibly_damaging(0.474) | TCGA-EW-A1OZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | trastuzumab | SD |
| PTPRN2 | deletion | Frame_Shift_Del | c.2305delN | p.Glu769ArgfsTer12 | p.E769Rfs*12 | Q92932 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |||
| PTPRN2 | SNV | Missense_Mutation | rs376560632 | c.2701C>T | p.Arg901Cys | p.R901C | Q92932 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 |
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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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