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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:00160557 | Cervix | CC | Wnt signaling pathway | 98/2311 | 444/18723 | 4.82e-09 | 4.65e-07 | 98 |
| GO:01987387 | Cervix | CC | cell-cell signaling by wnt | 98/2311 | 446/18723 | 6.16e-09 | 5.58e-07 | 98 |
| GO:200005810 | Cervix | CC | regulation of ubiquitin-dependent protein catabolic process | 47/2311 | 164/18723 | 1.63e-08 | 1.25e-06 | 47 |
| GO:004316110 | Cervix | CC | proteasome-mediated ubiquitin-dependent protein catabolic process | 91/2311 | 412/18723 | 1.65e-08 | 1.25e-06 | 91 |
| GO:00301117 | Cervix | CC | regulation of Wnt signaling pathway | 76/2311 | 328/18723 | 3.05e-08 | 2.08e-06 | 76 |
| GO:003133110 | Cervix | CC | positive regulation of cellular catabolic process | 91/2311 | 427/18723 | 9.64e-08 | 5.25e-06 | 91 |
| GO:00002097 | Cervix | CC | protein polyubiquitination | 58/2311 | 236/18723 | 1.57e-07 | 7.41e-06 | 58 |
| GO:190336410 | Cervix | CC | positive regulation of cellular protein catabolic process | 43/2311 | 155/18723 | 1.80e-07 | 8.28e-06 | 43 |
| GO:006113610 | Cervix | CC | regulation of proteasomal protein catabolic process | 48/2311 | 187/18723 | 4.63e-07 | 1.77e-05 | 48 |
| GO:003243410 | Cervix | CC | regulation of proteasomal ubiquitin-dependent protein catabolic process | 38/2311 | 134/18723 | 4.99e-07 | 1.88e-05 | 38 |
| GO:19030528 | Cervix | CC | positive regulation of proteolysis involved in cellular protein catabolic process | 34/2311 | 133/18723 | 2.28e-05 | 4.01e-04 | 34 |
| GO:200006010 | Cervix | CC | positive regulation of ubiquitin-dependent protein catabolic process | 29/2311 | 107/18723 | 2.77e-05 | 4.62e-04 | 29 |
| GO:00324369 | Cervix | CC | positive regulation of proteasomal ubiquitin-dependent protein catabolic process | 25/2311 | 90/18723 | 6.22e-05 | 8.90e-04 | 25 |
| GO:19018008 | Cervix | CC | positive regulation of proteasomal protein catabolic process | 29/2311 | 114/18723 | 9.71e-05 | 1.27e-03 | 29 |
| GO:00301784 | Cervix | CC | negative regulation of Wnt signaling pathway | 35/2311 | 170/18723 | 1.52e-03 | 1.17e-02 | 35 |
| GO:00518656 | Cervix | CC | protein autoubiquitination | 17/2311 | 73/18723 | 6.71e-03 | 3.70e-02 | 17 |
| GO:00482851 | Cervix | CC | organelle fission | 78/2311 | 488/18723 | 9.70e-03 | 4.79e-02 | 78 |
| GO:00182054 | Cervix | CC | peptidyl-lysine modification | 62/2311 | 376/18723 | 1.04e-02 | 4.97e-02 | 62 |
| GO:0051258 | Colorectum | AD | protein polymerization | 112/3918 | 297/18723 | 1.85e-11 | 2.27e-09 | 112 |
| GO:0031647 | Colorectum | AD | regulation of protein stability | 108/3918 | 298/18723 | 6.33e-10 | 5.08e-08 | 108 |
| 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 |
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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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