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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 |
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| 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:0009743 | Colorectum | AD | response to carbohydrate | 86/3918 | 253/18723 | 8.43e-07 | 2.90e-05 | 86 |
| GO:0043087 | Colorectum | AD | regulation of GTPase activity | 110/3918 | 348/18723 | 1.64e-06 | 5.03e-05 | 110 |
| GO:0034284 | Colorectum | AD | response to monosaccharide | 76/3918 | 225/18723 | 4.64e-06 | 1.23e-04 | 76 |
| GO:0033500 | Colorectum | AD | carbohydrate homeostasis | 84/3918 | 259/18723 | 9.10e-06 | 2.15e-04 | 84 |
| GO:0009746 | Colorectum | AD | response to hexose | 73/3918 | 219/18723 | 1.20e-05 | 2.65e-04 | 73 |
| GO:0009749 | Colorectum | AD | response to glucose | 71/3918 | 212/18723 | 1.31e-05 | 2.85e-04 | 71 |
| GO:0042593 | Colorectum | AD | glucose homeostasis | 83/3918 | 258/18723 | 1.44e-05 | 3.11e-04 | 83 |
| GO:0001678 | Colorectum | AD | cellular glucose homeostasis | 60/3918 | 172/18723 | 1.49e-05 | 3.18e-04 | 60 |
| 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:0071322 | Colorectum | AD | cellular response to carbohydrate stimulus | 56/3918 | 163/18723 | 4.61e-05 | 7.97e-04 | 56 |
| GO:0071333 | Colorectum | AD | cellular response to glucose stimulus | 52/3918 | 151/18723 | 7.88e-05 | 1.25e-03 | 52 |
| GO:0009306 | Colorectum | AD | protein secretion | 105/3918 | 359/18723 | 1.05e-04 | 1.57e-03 | 105 |
| GO:0071331 | Colorectum | AD | cellular response to hexose stimulus | 52/3918 | 153/18723 | 1.16e-04 | 1.71e-03 | 52 |
| GO:0035592 | Colorectum | AD | establishment of protein localization to extracellular region | 105/3918 | 360/18723 | 1.18e-04 | 1.73e-03 | 105 |
| GO:0071326 | Colorectum | AD | cellular response to monosaccharide stimulus | 52/3918 | 154/18723 | 1.40e-04 | 1.98e-03 | 52 |
| GO:0071692 | Colorectum | AD | protein localization to extracellular region | 106/3918 | 368/18723 | 1.86e-04 | 2.49e-03 | 106 |
| GO:0030073 | Colorectum | AD | insulin secretion | 61/3918 | 195/18723 | 4.28e-04 | 4.81e-03 | 61 |
| GO:0015833 | Colorectum | AD | peptide transport | 77/3918 | 264/18723 | 8.90e-04 | 8.60e-03 | 77 |
| GO:0035773 | Colorectum | AD | insulin secretion involved in cellular response to glucose stimulus | 27/3918 | 73/18723 | 1.17e-03 | 1.05e-02 | 27 |
| 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 | novel | c.2236G>C | p.Glu746Gln | p.E746Q | Q92932 | protein_coding | tolerated(0.14) | benign(0.084) | TCGA-96-A4JK-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | gemcitabine | CR |
| PTPRN2 | SNV | Missense_Mutation | novel | c.2856N>A | p.Ser952Arg | p.S952R | Q92932 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-NC-A5HD-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| PTPRN2 | SNV | Missense_Mutation | novel | c.2598N>A | p.Asn866Lys | p.N866K | Q92932 | protein_coding | deleterious(0) | benign(0.41) | TCGA-NC-A5HE-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | CR |
| PTPRN2 | SNV | Missense_Mutation | novel | c.1495N>G | p.Leu499Val | p.L499V | Q92932 | protein_coding | tolerated(0.1) | benign(0.057) | TCGA-NC-A5HN-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| PTPRN2 | SNV | Missense_Mutation | novel | c.2362N>A | p.Leu788Met | p.L788M | Q92932 | protein_coding | tolerated(0.2) | possibly_damaging(0.731) | TCGA-O2-A52Q-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| PTPRN2 | deletion | Frame_Shift_Del | novel | c.1280_1295delAGTCCGAGCACCCTGA | p.Lys427SerfsTer84 | p.K427Sfs*84 | Q92932 | protein_coding | TCGA-22-1016-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
| PTPRN2 | SNV | Missense_Mutation | novel | c.530A>G | p.Gln177Arg | p.Q177R | Q92932 | protein_coding | tolerated(0.48) | benign(0.01) | TCGA-BA-4078-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| PTPRN2 | SNV | Missense_Mutation | c.2792A>G | p.Asn931Ser | p.N931S | Q92932 | protein_coding | deleterious(0.02) | possibly_damaging(0.807) | TCGA-CR-7402-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | SD | |
| PTPRN2 | SNV | Missense_Mutation | novel | c.570N>C | p.Glu190Asp | p.E190D | Q92932 | protein_coding | tolerated(1) | benign(0.003) | TCGA-TN-A7HL-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | CR |
| PTPRN2 | SNV | Missense_Mutation | c.191T>C | p.Val64Ala | p.V64A | Q92932 | protein_coding | tolerated(0.33) | benign(0.026) | TCGA-B7-5816-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| 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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