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Gene: NF2 |
Gene summary for NF2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NF2 | Gene ID | 4771 |
| Gene name | neurofibromin 2 | |
| Gene Alias | ACN | |
| Cytomap | 22q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | A0A024R1J8 |
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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 |
| 4771 | NF2 | LZE24T | Human | Esophagus | ESCC | 4.83e-03 | 1.09e-01 | 0.0596 |
| 4771 | NF2 | P2T-E | Human | Esophagus | ESCC | 4.56e-16 | 2.22e-01 | 0.1177 |
| 4771 | NF2 | P4T-E | Human | Esophagus | ESCC | 1.59e-12 | 2.87e-01 | 0.1323 |
| 4771 | NF2 | P8T-E | Human | Esophagus | ESCC | 5.81e-11 | 1.83e-01 | 0.0889 |
| 4771 | NF2 | P9T-E | Human | Esophagus | ESCC | 1.10e-04 | 1.08e-01 | 0.1131 |
| 4771 | NF2 | P10T-E | Human | Esophagus | ESCC | 1.71e-12 | 2.54e-01 | 0.116 |
| 4771 | NF2 | P11T-E | Human | Esophagus | ESCC | 4.09e-04 | 1.37e-01 | 0.1426 |
| 4771 | NF2 | P12T-E | Human | Esophagus | ESCC | 1.76e-05 | 1.60e-01 | 0.1122 |
| 4771 | NF2 | P15T-E | Human | Esophagus | ESCC | 1.01e-08 | 1.90e-01 | 0.1149 |
| 4771 | NF2 | P16T-E | Human | Esophagus | ESCC | 6.54e-16 | 1.95e-01 | 0.1153 |
| 4771 | NF2 | P17T-E | Human | Esophagus | ESCC | 5.11e-10 | 4.29e-01 | 0.1278 |
| 4771 | NF2 | P19T-E | Human | Esophagus | ESCC | 1.18e-08 | 3.65e-01 | 0.1662 |
| 4771 | NF2 | P20T-E | Human | Esophagus | ESCC | 2.72e-05 | 1.25e-01 | 0.1124 |
| 4771 | NF2 | P21T-E | Human | Esophagus | ESCC | 1.30e-09 | 1.97e-01 | 0.1617 |
| 4771 | NF2 | P22T-E | Human | Esophagus | ESCC | 1.34e-12 | 2.28e-01 | 0.1236 |
| 4771 | NF2 | P23T-E | Human | Esophagus | ESCC | 6.91e-04 | 1.38e-01 | 0.108 |
| 4771 | NF2 | P24T-E | Human | Esophagus | ESCC | 3.17e-07 | 1.64e-01 | 0.1287 |
| 4771 | NF2 | P26T-E | Human | Esophagus | ESCC | 7.27e-12 | 3.00e-01 | 0.1276 |
| 4771 | NF2 | P27T-E | Human | Esophagus | ESCC | 2.03e-14 | 2.01e-01 | 0.1055 |
| 4771 | NF2 | P28T-E | Human | Esophagus | ESCC | 2.19e-06 | 1.53e-01 | 0.1149 |
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| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:00000705 | Thyroid | PTC | mitotic sister chromatid segregation | 79/5968 | 168/18723 | 2.78e-05 | 2.71e-04 | 79 |
| GO:003223323 | Thyroid | PTC | positive regulation of actin filament bundle assembly | 36/5968 | 63/18723 | 2.98e-05 | 2.86e-04 | 36 |
| GO:00070595 | Thyroid | PTC | chromosome segregation | 146/5968 | 346/18723 | 2.99e-05 | 2.87e-04 | 146 |
| GO:00008196 | Thyroid | PTC | sister chromatid segregation | 92/5968 | 202/18723 | 3.07e-05 | 2.94e-04 | 92 |
| GO:19019917 | Thyroid | PTC | negative regulation of mitotic cell cycle phase transition | 83/5968 | 179/18723 | 3.34e-05 | 3.17e-04 | 83 |
| GO:00518659 | Thyroid | PTC | protein autoubiquitination | 40/5968 | 73/18723 | 4.17e-05 | 3.80e-04 | 40 |
| GO:001657110 | Thyroid | PTC | histone methylation | 67/5968 | 141/18723 | 7.31e-05 | 6.31e-04 | 67 |
| GO:00322009 | Thyroid | PTC | telomere organization | 74/5968 | 159/18723 | 7.46e-05 | 6.43e-04 | 74 |
| GO:000736910 | Thyroid | PTC | gastrulation | 84/5968 | 185/18723 | 7.58e-05 | 6.52e-04 | 84 |
| GO:0071897110 | Thyroid | PTC | DNA biosynthetic process | 82/5968 | 180/18723 | 7.98e-05 | 6.81e-04 | 82 |
| GO:000647910 | Thyroid | PTC | protein methylation | 82/5968 | 181/18723 | 1.01e-04 | 8.21e-04 | 82 |
| GO:000821310 | Thyroid | PTC | protein alkylation | 82/5968 | 181/18723 | 1.01e-04 | 8.21e-04 | 82 |
| GO:005149615 | Thyroid | PTC | positive regulation of stress fiber assembly | 30/5968 | 52/18723 | 1.06e-04 | 8.56e-04 | 30 |
| GO:000283114 | Thyroid | PTC | regulation of response to biotic stimulus | 136/5968 | 327/18723 | 1.22e-04 | 9.69e-04 | 136 |
| GO:00467858 | Thyroid | PTC | microtubule polymerization | 43/5968 | 83/18723 | 1.26e-04 | 9.98e-04 | 43 |
| GO:00310606 | Thyroid | PTC | regulation of histone methylation | 37/5968 | 69/18723 | 1.46e-04 | 1.13e-03 | 37 |
| GO:00169256 | Thyroid | PTC | protein sumoylation | 30/5968 | 53/18723 | 1.71e-04 | 1.31e-03 | 30 |
| GO:00519608 | Thyroid | PTC | regulation of nervous system development | 177/5968 | 443/18723 | 1.72e-04 | 1.32e-03 | 177 |
| GO:005122514 | Thyroid | PTC | spindle assembly | 56/5968 | 117/18723 | 2.17e-04 | 1.60e-03 | 56 |
| GO:003532912 | Thyroid | PTC | hippo signaling | 24/5968 | 40/18723 | 2.27e-04 | 1.65e-03 | 24 |
| 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 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04530211 | Esophagus | ESCC | Tight junction | 105/4205 | 169/8465 | 6.73e-04 | 2.23e-03 | 1.14e-03 | 105 |
| hsa0439018 | Esophagus | ESCC | Hippo signaling pathway | 92/4205 | 157/8465 | 1.46e-02 | 3.31e-02 | 1.69e-02 | 92 |
| hsa04530310 | Esophagus | ESCC | Tight junction | 105/4205 | 169/8465 | 6.73e-04 | 2.23e-03 | 1.14e-03 | 105 |
| hsa0439019 | Esophagus | ESCC | Hippo signaling pathway | 92/4205 | 157/8465 | 1.46e-02 | 3.31e-02 | 1.69e-02 | 92 |
| hsa0453030 | Oral cavity | OSCC | Tight junction | 102/3704 | 169/8465 | 8.68e-06 | 3.93e-05 | 2.00e-05 | 102 |
| hsa0439016 | Oral cavity | OSCC | Hippo signaling pathway | 86/3704 | 157/8465 | 3.30e-03 | 8.24e-03 | 4.20e-03 | 86 |
| hsa04530114 | Oral cavity | OSCC | Tight junction | 102/3704 | 169/8465 | 8.68e-06 | 3.93e-05 | 2.00e-05 | 102 |
| hsa0439017 | Oral cavity | OSCC | Hippo signaling pathway | 86/3704 | 157/8465 | 3.30e-03 | 8.24e-03 | 4.20e-03 | 86 |
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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. |
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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 |
| NF2 | SNV | Missense_Mutation | c.645N>C | p.Glu215Asp | p.E215D | P35240 | protein_coding | tolerated(0.61) | benign(0.003) | TCGA-BH-A0C7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR | |
| NF2 | SNV | Missense_Mutation | c.17N>T | p.Ala6Val | p.A6V | P35240 | protein_coding | deleterious_low_confidence(0.01) | benign(0.023) | TCGA-C5-A7CO-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | SD | |
| NF2 | SNV | Missense_Mutation | rs74315503 | c.1387N>A | p.Glu463Lys | p.E463K | P35240 | protein_coding | tolerated(0.49) | benign(0.311) | TCGA-C5-A8XK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| NF2 | SNV | Missense_Mutation | rs765386271 | c.1672N>G | p.Leu558Val | p.L558V | P35240 | protein_coding | tolerated(0.08) | possibly_damaging(0.528) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD |
| NF2 | SNV | Missense_Mutation | novel | c.746N>A | p.Arg249Lys | p.R249K | P35240 | protein_coding | tolerated(1) | benign(0.003) | TCGA-VS-A94Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NF2 | SNV | Missense_Mutation | rs776109136 | c.1391N>T | p.Ala464Val | p.A464V | P35240 | protein_coding | deleterious(0.01) | possibly_damaging(0.798) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| NF2 | SNV | Missense_Mutation | c.813N>G | p.Phe271Leu | p.F271L | P35240 | protein_coding | tolerated(0.15) | benign(0.411) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| NF2 | SNV | Missense_Mutation | c.1075A>T | p.Arg359Trp | p.R359W | P35240 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AU-6004-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NF2 | SNV | Missense_Mutation | novel | c.275N>C | p.Val92Ala | p.V92A | P35240 | protein_coding | tolerated(0.28) | benign(0.396) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| NF2 | SNV | Missense_Mutation | novel | c.369N>T | p.Lys123Asn | p.K123N | P35240 | protein_coding | deleterious(0.02) | probably_damaging(0.918) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| Page: 1 2 3 4 5 6 |
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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 |
| 4771 | NF2 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, DRUG RESISTANCE, KINASE | SELUMETINIB | SELUMETINIB | 26359368 | |
| 4771 | NF2 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, DRUG RESISTANCE, KINASE | EVEROLIMUS | EVEROLIMUS | 25567352 | |
| 4771 | NF2 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, DRUG RESISTANCE, KINASE | TEMSIROLIMUS | TEMSIROLIMUS | 25878190 | |
| 4771 | NF2 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, DRUG RESISTANCE, KINASE | CISPLATIN | CISPLATIN | 25798586 | |
| 4771 | NF2 | CLINICALLY ACTIONABLE, TUMOR SUPPRESSOR, DRUG RESISTANCE, KINASE | CARBOPLATIN | CARBOPLATIN | 25798586 |
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