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Gene: NTRK2 |
Gene summary for NTRK2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NTRK2 | Gene ID | 4915 |
| Gene name | neurotrophic receptor tyrosine kinase 2 | |
| Gene Alias | DEE58 | |
| Cytomap | 9q21.33 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q16620 |
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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 |
| 4915 | NTRK2 | GSM4909281 | Human | Breast | IDC | 7.11e-10 | -3.33e-01 | 0.21 |
| 4915 | NTRK2 | GSM4909285 | Human | Breast | IDC | 1.62e-07 | -2.65e-01 | 0.21 |
| 4915 | NTRK2 | GSM4909286 | Human | Breast | IDC | 3.60e-11 | -3.34e-01 | 0.1081 |
| 4915 | NTRK2 | GSM4909290 | Human | Breast | IDC | 1.80e-10 | -3.77e-01 | 0.2096 |
| 4915 | NTRK2 | GSM4909291 | Human | Breast | IDC | 1.24e-04 | -3.53e-01 | 0.1753 |
| 4915 | NTRK2 | GSM4909293 | Human | Breast | IDC | 1.29e-13 | -2.98e-01 | 0.1581 |
| 4915 | NTRK2 | GSM4909294 | Human | Breast | IDC | 7.50e-16 | -3.52e-01 | 0.2022 |
| 4915 | NTRK2 | GSM4909296 | Human | Breast | IDC | 3.13e-15 | -3.56e-01 | 0.1524 |
| 4915 | NTRK2 | GSM4909297 | Human | Breast | IDC | 3.01e-16 | -3.71e-01 | 0.1517 |
| 4915 | NTRK2 | GSM4909298 | Human | Breast | IDC | 3.03e-12 | -3.05e-01 | 0.1551 |
| 4915 | NTRK2 | GSM4909299 | Human | Breast | IDC | 3.64e-27 | 7.93e-01 | 0.035 |
| 4915 | NTRK2 | GSM4909301 | Human | Breast | IDC | 1.24e-19 | -3.77e-01 | 0.1577 |
| 4915 | NTRK2 | GSM4909302 | Human | Breast | IDC | 5.84e-08 | -3.45e-01 | 0.1545 |
| 4915 | NTRK2 | GSM4909304 | Human | Breast | IDC | 1.58e-16 | -3.72e-01 | 0.1636 |
| 4915 | NTRK2 | GSM4909306 | Human | Breast | IDC | 1.51e-06 | -2.78e-01 | 0.1564 |
| 4915 | NTRK2 | GSM4909311 | Human | Breast | IDC | 2.20e-19 | -3.38e-01 | 0.1534 |
| 4915 | NTRK2 | GSM4909312 | Human | Breast | IDC | 2.86e-19 | -3.77e-01 | 0.1552 |
| 4915 | NTRK2 | GSM4909315 | Human | Breast | IDC | 3.85e-17 | -3.65e-01 | 0.21 |
| 4915 | NTRK2 | GSM4909316 | Human | Breast | IDC | 2.04e-03 | -3.77e-01 | 0.21 |
| 4915 | NTRK2 | GSM4909319 | Human | Breast | IDC | 6.92e-19 | -3.42e-01 | 0.1563 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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:00709979 | Breast | Precancer | neuron death | 50/1080 | 361/18723 | 7.75e-09 | 5.70e-07 | 50 |
| GO:00514029 | Breast | Precancer | neuron apoptotic process | 38/1080 | 246/18723 | 2.68e-08 | 1.75e-06 | 38 |
| GO:19012149 | Breast | Precancer | regulation of neuron death | 41/1080 | 319/18723 | 1.27e-06 | 4.80e-05 | 41 |
| GO:00435237 | Breast | Precancer | regulation of neuron apoptotic process | 31/1080 | 212/18723 | 1.69e-06 | 6.08e-05 | 31 |
| GO:00420633 | Breast | Precancer | gliogenesis | 33/1080 | 301/18723 | 3.06e-04 | 4.40e-03 | 33 |
| GO:00435243 | Breast | Precancer | negative regulation of neuron apoptotic process | 19/1080 | 145/18723 | 6.83e-04 | 8.34e-03 | 19 |
| GO:19012157 | Breast | Precancer | negative regulation of neuron death | 24/1080 | 208/18723 | 9.50e-04 | 1.07e-02 | 24 |
| GO:00100013 | Breast | Precancer | glial cell differentiation | 25/1080 | 225/18723 | 1.29e-03 | 1.37e-02 | 25 |
| GO:00434912 | Breast | Precancer | protein kinase B signaling | 23/1080 | 211/18723 | 2.53e-03 | 2.30e-02 | 23 |
| GO:00336749 | Breast | Precancer | positive regulation of kinase activity | 42/1080 | 467/18723 | 2.94e-03 | 2.54e-02 | 42 |
| GO:19900908 | Breast | Precancer | cellular response to nerve growth factor stimulus | 9/1080 | 53/18723 | 3.05e-03 | 2.62e-02 | 9 |
| GO:19900896 | Breast | Precancer | response to nerve growth factor | 9/1080 | 56/18723 | 4.47e-03 | 3.47e-02 | 9 |
| GO:00011015 | Breast | Precancer | response to acid chemical | 16/1080 | 135/18723 | 4.85e-03 | 3.67e-02 | 16 |
| GO:0021782 | Breast | Precancer | glial cell development | 14/1080 | 116/18723 | 6.92e-03 | 4.67e-02 | 14 |
| GO:007099714 | Breast | IDC | neuron death | 57/1434 | 361/18723 | 1.31e-07 | 7.38e-06 | 57 |
| GO:005140213 | Breast | IDC | neuron apoptotic process | 42/1434 | 246/18723 | 7.21e-07 | 3.35e-05 | 42 |
| GO:190121414 | Breast | IDC | regulation of neuron death | 48/1434 | 319/18723 | 5.01e-06 | 1.69e-04 | 48 |
| GO:004352313 | Breast | IDC | regulation of neuron apoptotic process | 35/1434 | 212/18723 | 1.26e-05 | 3.29e-04 | 35 |
| GO:004352411 | Breast | IDC | negative regulation of neuron apoptotic process | 23/1434 | 145/18723 | 6.58e-04 | 8.11e-03 | 23 |
| GO:004206311 | Breast | IDC | gliogenesis | 39/1434 | 301/18723 | 8.63e-04 | 1.00e-02 | 39 |
| 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0472214 | Cervix | CC | Neurotrophin signaling pathway | 32/1267 | 119/8465 | 5.01e-04 | 2.42e-03 | 1.43e-03 | 32 |
| hsa040142 | Cervix | CC | Ras signaling pathway | 51/1267 | 236/8465 | 3.55e-03 | 1.34e-02 | 7.91e-03 | 51 |
| hsa040109 | Cervix | CC | MAPK signaling pathway | 62/1267 | 302/8465 | 4.89e-03 | 1.67e-02 | 9.86e-03 | 62 |
| hsa0472215 | Cervix | CC | Neurotrophin signaling pathway | 32/1267 | 119/8465 | 5.01e-04 | 2.42e-03 | 1.43e-03 | 32 |
| hsa0401411 | Cervix | CC | Ras signaling pathway | 51/1267 | 236/8465 | 3.55e-03 | 1.34e-02 | 7.91e-03 | 51 |
| hsa0401012 | Cervix | CC | MAPK signaling pathway | 62/1267 | 302/8465 | 4.89e-03 | 1.67e-02 | 9.86e-03 | 62 |
| hsa04722 | Colorectum | AD | Neurotrophin signaling pathway | 50/2092 | 119/8465 | 2.28e-05 | 2.24e-04 | 1.43e-04 | 50 |
| hsa047221 | Colorectum | AD | Neurotrophin signaling pathway | 50/2092 | 119/8465 | 2.28e-05 | 2.24e-04 | 1.43e-04 | 50 |
| hsa0472225 | Esophagus | ESCC | Neurotrophin signaling pathway | 80/4205 | 119/8465 | 7.33e-05 | 3.07e-04 | 1.57e-04 | 80 |
| hsa041517 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
| hsa04722111 | Esophagus | ESCC | Neurotrophin signaling pathway | 80/4205 | 119/8465 | 7.33e-05 | 3.07e-04 | 1.57e-04 | 80 |
| hsa0415114 | Esophagus | ESCC | PI3K-Akt signaling pathway | 197/4205 | 354/8465 | 1.24e-02 | 2.83e-02 | 1.45e-02 | 197 |
| hsa0472220 | Oral cavity | OSCC | Neurotrophin signaling pathway | 74/3704 | 119/8465 | 3.55e-05 | 1.49e-04 | 7.58e-05 | 74 |
| hsa0401014 | Oral cavity | OSCC | MAPK signaling pathway | 165/3704 | 302/8465 | 7.11e-05 | 2.74e-04 | 1.40e-04 | 165 |
| hsa041516 | Oral cavity | OSCC | PI3K-Akt signaling pathway | 185/3704 | 354/8465 | 6.26e-04 | 1.86e-03 | 9.49e-04 | 185 |
| hsa04722110 | Oral cavity | OSCC | Neurotrophin signaling pathway | 74/3704 | 119/8465 | 3.55e-05 | 1.49e-04 | 7.58e-05 | 74 |
| hsa0401015 | Oral cavity | OSCC | MAPK signaling pathway | 165/3704 | 302/8465 | 7.11e-05 | 2.74e-04 | 1.40e-04 | 165 |
| hsa0415113 | Oral cavity | OSCC | PI3K-Akt signaling pathway | 185/3704 | 354/8465 | 6.26e-04 | 1.86e-03 | 9.49e-04 | 185 |
| hsa0472224 | Oral cavity | LP | Neurotrophin signaling pathway | 46/2418 | 119/8465 | 1.07e-02 | 3.77e-02 | 2.43e-02 | 46 |
| hsa0472234 | Oral cavity | LP | Neurotrophin signaling pathway | 46/2418 | 119/8465 | 1.07e-02 | 3.77e-02 | 2.43e-02 | 46 |
| Page: 1 2 |
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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 |
| NTF3 | NTRK2 | NTF3_NTRK2 | NT | Endometrium | ADJ |
| BDNF | NTRK2 | BDNF_NTRK2 | NT | Esophagus | ESCC |
| NTF4 | NTRK2 | NTF5_NTRK2 | NT | Esophagus | ESCC |
| NTF4 | NTRK2 | NTF5_NTRK2 | NT | HNSCC | Precancer |
| NTF3 | NTRK2 | NTF3_NTRK2 | NT | Liver | Healthy |
| 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 |
| NTRK2 | SNV | Missense_Mutation | c.250N>A | p.Glu84Lys | p.E84K | Q16620 | protein_coding | tolerated(0.69) | benign(0.405) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| NTRK2 | SNV | Missense_Mutation | c.41G>A | p.Arg14Gln | p.R14Q | Q16620 | protein_coding | tolerated_low_confidence(0.37) | benign(0.173) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NTRK2 | SNV | Missense_Mutation | c.1741G>A | p.Asp581Asn | p.D581N | Q16620 | protein_coding | deleterious(0.02) | benign(0.015) | TCGA-A6-3810-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| NTRK2 | SNV | Missense_Mutation | c.669N>A | p.Asp223Glu | p.D223E | Q16620 | protein_coding | tolerated(0.81) | benign(0.007) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| NTRK2 | SNV | Missense_Mutation | c.638N>T | p.Ser213Phe | p.S213F | Q16620 | protein_coding | deleterious(0.02) | possibly_damaging(0.906) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NTRK2 | SNV | Missense_Mutation | rs551310223 | c.1160N>A | p.Gly387Asp | p.G387D | Q16620 | protein_coding | tolerated(0.51) | benign(0.001) | TCGA-AA-3494-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folinic | PR |
| NTRK2 | SNV | Missense_Mutation | novel | c.710N>T | p.Ser237Phe | p.S237F | Q16620 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| NTRK2 | SNV | Missense_Mutation | novel | c.2288N>G | p.Phe763Cys | p.F763C | Q16620 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3862-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| NTRK2 | SNV | Missense_Mutation | rs201491838 | c.2357G>A | p.Arg786Gln | p.R786Q | Q16620 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| NTRK2 | SNV | Missense_Mutation | c.2194N>T | p.Pro732Ser | p.P732S | Q16620 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
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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 |
| 4915 | NTRK2 | KINASE, TYROSINE KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | Macrocycle derivative 13 | |||
| 4915 | NTRK2 | KINASE, TYROSINE KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | 249565751 | ||
| 4915 | NTRK2 | KINASE, TYROSINE KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | 249565869 | CEP-11981 | |
| 4915 | NTRK2 | KINASE, TYROSINE KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | lithium | LITHIUM | 21047205,24885933 | |
| 4915 | NTRK2 | KINASE, TYROSINE KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | 381744997 | REPOTRECTINIB | |
| 4915 | NTRK2 | KINASE, TYROSINE KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | PILOCARPINE | PILOCARPINE | 15183516 | |
| 4915 | NTRK2 | KINASE, TYROSINE KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | AST-487 | AST-487 | ||
| 4915 | NTRK2 | KINASE, TYROSINE KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | CHEMBL3545179 | AZD-7451 | |
| 4915 | NTRK2 | KINASE, TYROSINE KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | 223366033 | ||
| 4915 | NTRK2 | KINASE, TYROSINE KINASE, ENZYME, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | TCMDC-125758 | CHEMBL546797 |
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