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Gene: NPTN |
Gene summary for NPTN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NPTN | Gene ID | 27020 |
| Gene name | neuroplastin | |
| Gene Alias | GP55 | |
| Cytomap | 15q24.1 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q9Y639 |
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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 |
| 27020 | NPTN | LZE2D | Human | Esophagus | HGIN | 4.96e-03 | 5.27e-02 | 0.0642 |
| 27020 | NPTN | LZE4T | Human | Esophagus | ESCC | 5.95e-08 | 1.89e-01 | 0.0811 |
| 27020 | NPTN | LZE8T | Human | Esophagus | ESCC | 4.02e-02 | 1.16e-03 | 0.067 |
| 27020 | NPTN | LZE24T | Human | Esophagus | ESCC | 1.86e-09 | 3.38e-01 | 0.0596 |
| 27020 | NPTN | LZE21T | Human | Esophagus | ESCC | 8.76e-04 | -3.89e-03 | 0.0655 |
| 27020 | NPTN | P2T-E | Human | Esophagus | ESCC | 6.78e-18 | 2.04e-01 | 0.1177 |
| 27020 | NPTN | P4T-E | Human | Esophagus | ESCC | 1.78e-21 | 5.81e-01 | 0.1323 |
| 27020 | NPTN | P5T-E | Human | Esophagus | ESCC | 6.06e-19 | -7.36e-02 | 0.1327 |
| 27020 | NPTN | P8T-E | Human | Esophagus | ESCC | 1.61e-55 | 1.52e+00 | 0.0889 |
| 27020 | NPTN | P9T-E | Human | Esophagus | ESCC | 7.76e-08 | 2.72e-01 | 0.1131 |
| 27020 | NPTN | P10T-E | Human | Esophagus | ESCC | 4.18e-31 | 6.34e-01 | 0.116 |
| 27020 | NPTN | P11T-E | Human | Esophagus | ESCC | 2.18e-16 | 2.82e-01 | 0.1426 |
| 27020 | NPTN | P12T-E | Human | Esophagus | ESCC | 3.60e-23 | 4.26e-01 | 0.1122 |
| 27020 | NPTN | P15T-E | Human | Esophagus | ESCC | 1.38e-19 | 4.45e-01 | 0.1149 |
| 27020 | NPTN | P16T-E | Human | Esophagus | ESCC | 4.79e-14 | 1.12e-01 | 0.1153 |
| 27020 | NPTN | P19T-E | Human | Esophagus | ESCC | 3.28e-08 | 1.37e-01 | 0.1662 |
| 27020 | NPTN | P20T-E | Human | Esophagus | ESCC | 1.24e-11 | 2.07e-01 | 0.1124 |
| 27020 | NPTN | P21T-E | Human | Esophagus | ESCC | 7.58e-21 | 3.76e-01 | 0.1617 |
| 27020 | NPTN | P22T-E | Human | Esophagus | ESCC | 7.30e-15 | 1.88e-01 | 0.1236 |
| 27020 | NPTN | P23T-E | Human | Esophagus | ESCC | 6.98e-16 | 5.27e-01 | 0.108 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:001097514 | Prostate | Tumor | regulation of neuron projection development | 115/3246 | 445/18723 | 3.34e-06 | 5.44e-05 | 115 |
| GO:003134614 | Prostate | Tumor | positive regulation of cell projection organization | 94/3246 | 353/18723 | 6.96e-06 | 1.05e-04 | 94 |
| GO:005076911 | Prostate | Tumor | positive regulation of neurogenesis | 64/3246 | 225/18723 | 2.26e-05 | 2.88e-04 | 64 |
| GO:005076711 | Prostate | Tumor | regulation of neurogenesis | 93/3246 | 364/18723 | 4.45e-05 | 5.02e-04 | 93 |
| GO:005080813 | Prostate | Tumor | synapse organization | 105/3246 | 426/18723 | 7.20e-05 | 7.62e-04 | 105 |
| GO:006156413 | Prostate | Tumor | axon development | 113/3246 | 467/18723 | 8.86e-05 | 8.74e-04 | 113 |
| GO:000931415 | Prostate | Tumor | response to radiation | 109/3246 | 456/18723 | 1.94e-04 | 1.70e-03 | 109 |
| GO:003150312 | Prostate | Tumor | protein-containing complex localization | 59/3246 | 220/18723 | 2.71e-04 | 2.24e-03 | 59 |
| GO:000740913 | Prostate | Tumor | axonogenesis | 100/3246 | 418/18723 | 3.38e-04 | 2.70e-03 | 100 |
| GO:005196211 | Prostate | Tumor | positive regulation of nervous system development | 69/3246 | 272/18723 | 4.99e-04 | 3.67e-03 | 69 |
| GO:004341012 | Prostate | Tumor | positive regulation of MAPK cascade | 110/3246 | 480/18723 | 9.41e-04 | 6.18e-03 | 110 |
| GO:00902871 | Prostate | Tumor | regulation of cellular response to growth factor stimulus | 74/3246 | 304/18723 | 1.13e-03 | 7.22e-03 | 74 |
| GO:005196011 | Prostate | Tumor | regulation of nervous system development | 102/3246 | 443/18723 | 1.20e-03 | 7.60e-03 | 102 |
| GO:001097611 | Prostate | Tumor | positive regulation of neuron projection development | 42/3246 | 163/18723 | 4.24e-03 | 2.12e-02 | 42 |
| GO:007037113 | Prostate | Tumor | ERK1 and ERK2 cascade | 76/3246 | 330/18723 | 4.66e-03 | 2.29e-02 | 76 |
| GO:00508901 | Prostate | Tumor | cognition | 69/3246 | 296/18723 | 5.03e-03 | 2.45e-02 | 69 |
| GO:00717741 | Prostate | Tumor | response to fibroblast growth factor | 31/3246 | 120/18723 | 1.22e-02 | 4.97e-02 | 31 |
| GO:003432919 | Skin | AK | cell junction assembly | 86/1910 | 420/18723 | 1.95e-10 | 2.68e-08 | 86 |
| GO:190382927 | Skin | AK | positive regulation of cellular protein localization | 64/1910 | 276/18723 | 2.23e-10 | 3.00e-08 | 64 |
| GO:006156416 | Skin | AK | axon development | 91/1910 | 467/18723 | 8.60e-10 | 8.63e-08 | 91 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| NPTN | SNV | Missense_Mutation | c.712N>T | p.Pro238Ser | p.P238S | Q9Y639 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A2-A04W-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| NPTN | SNV | Missense_Mutation | novel | c.673N>A | p.Ala225Thr | p.A225T | Q9Y639 | protein_coding | tolerated(0.42) | possibly_damaging(0.537) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NPTN | SNV | Missense_Mutation | c.118G>C | p.Glu40Gln | p.E40Q | Q9Y639 | protein_coding | tolerated(1) | probably_damaging(0.998) | TCGA-DS-A0VM-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
| NPTN | SNV | Missense_Mutation | novel | c.782N>T | p.Ser261Leu | p.S261L | Q9Y639 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-EA-A1QS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| NPTN | SNV | Missense_Mutation | c.527N>A | p.Ser176Tyr | p.S176Y | Q9Y639 | protein_coding | tolerated(0.47) | benign(0.186) | TCGA-AA-A02H-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| NPTN | SNV | Missense_Mutation | c.1025N>A | p.Pro342His | p.P342H | Q9Y639 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | |
| NPTN | SNV | Missense_Mutation | novel | c.193N>C | p.Trp65Arg | p.W65R | Q9Y639 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD |
| NPTN | SNV | Missense_Mutation | c.418N>A | p.Ala140Thr | p.A140T | Q9Y639 | protein_coding | deleterious(0) | possibly_damaging(0.494) | TCGA-D5-6930-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| NPTN | SNV | Missense_Mutation | novel | c.1046A>C | p.Glu349Ala | p.E349A | Q9Y639 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NPTN | SNV | Missense_Mutation | c.527C>T | p.Ser176Phe | p.S176F | Q9Y639 | protein_coding | tolerated(0.27) | possibly_damaging(0.505) | TCGA-AG-A026-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | 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 |
| 27020 | NPTN | CELL SURFACE, DRUGGABLE GENOME | ANTISERUM | 9004047 | ||
| 27020 | NPTN | CELL SURFACE, DRUGGABLE GENOME | GP100 | 8779689 |
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