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Gene: NSUN2 |
Gene summary for NSUN2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NSUN2 | Gene ID | 54888 |
| Gene name | NOP2/Sun RNA methyltransferase 2 | |
| Gene Alias | MISU | |
| Cytomap | 5p15.31 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q08J23 |
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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 |
| 54888 | NSUN2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.00e-07 | 5.36e-01 | -0.0811 |
| 54888 | NSUN2 | HTA11_78_2000001011 | Human | Colorectum | AD | 2.32e-05 | 4.29e-01 | -0.1088 |
| 54888 | NSUN2 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.66e-14 | 5.13e-01 | -0.1954 |
| 54888 | NSUN2 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.16e-04 | 3.37e-01 | -0.1464 |
| 54888 | NSUN2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 8.90e-05 | 4.11e-01 | -0.059 |
| 54888 | NSUN2 | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.10e-03 | 3.70e-01 | 0.0338 |
| 54888 | NSUN2 | HTA11_6818_2000001011 | Human | Colorectum | AD | 9.21e-03 | 4.32e-01 | 0.0112 |
| 54888 | NSUN2 | HTA11_6818_2000001021 | Human | Colorectum | AD | 2.01e-02 | 3.25e-01 | 0.0588 |
| 54888 | NSUN2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.69e-06 | 3.98e-01 | 0.294 |
| 54888 | NSUN2 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 6.39e-04 | 7.74e-01 | 0.3487 |
| 54888 | NSUN2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 6.24e-06 | 4.58e-01 | 0.3859 |
| 54888 | NSUN2 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 8.46e-04 | 5.84e-01 | 0.2585 |
| 54888 | NSUN2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.79e-34 | 1.10e+00 | 0.3005 |
| 54888 | NSUN2 | A015-C-203 | Human | Colorectum | FAP | 8.85e-05 | -8.18e-02 | -0.1294 |
| 54888 | NSUN2 | A002-C-203 | Human | Colorectum | FAP | 2.10e-02 | -1.32e-01 | 0.2786 |
| 54888 | NSUN2 | A015-C-104 | Human | Colorectum | FAP | 1.66e-05 | -1.39e-01 | -0.1899 |
| 54888 | NSUN2 | A002-C-016 | Human | Colorectum | FAP | 2.72e-07 | -2.19e-01 | 0.0521 |
| 54888 | NSUN2 | A002-C-116 | Human | Colorectum | FAP | 9.90e-09 | -1.53e-01 | -0.0452 |
| 54888 | NSUN2 | F034 | Human | Colorectum | FAP | 8.94e-05 | -1.39e-01 | -0.0665 |
| 54888 | NSUN2 | LZE2T | Human | Esophagus | ESCC | 7.31e-04 | 4.89e-01 | 0.082 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:0009895 | Colorectum | AD | negative regulation of catabolic process | 124/3918 | 320/18723 | 1.66e-13 | 3.35e-11 | 124 |
| GO:0031330 | Colorectum | AD | negative regulation of cellular catabolic process | 104/3918 | 262/18723 | 2.66e-12 | 3.96e-10 | 104 |
| GO:0006401 | Colorectum | AD | RNA catabolic process | 102/3918 | 278/18723 | 8.64e-10 | 6.76e-08 | 102 |
| GO:0044270 | Colorectum | AD | cellular nitrogen compound catabolic process | 147/3918 | 451/18723 | 3.35e-09 | 2.23e-07 | 147 |
| GO:0046700 | Colorectum | AD | heterocycle catabolic process | 145/3918 | 445/18723 | 4.37e-09 | 2.84e-07 | 145 |
| GO:0034655 | Colorectum | AD | nucleobase-containing compound catabolic process | 133/3918 | 407/18723 | 1.56e-08 | 9.12e-07 | 133 |
| GO:0019439 | Colorectum | AD | aromatic compound catabolic process | 146/3918 | 467/18723 | 7.48e-08 | 3.84e-06 | 146 |
| GO:1901361 | Colorectum | AD | organic cyclic compound catabolic process | 153/3918 | 495/18723 | 8.23e-08 | 4.18e-06 | 153 |
| GO:0006913 | Colorectum | AD | nucleocytoplasmic transport | 102/3918 | 301/18723 | 1.00e-07 | 4.85e-06 | 102 |
| GO:0051169 | Colorectum | AD | nuclear transport | 102/3918 | 301/18723 | 1.00e-07 | 4.85e-06 | 102 |
| GO:0032386 | Colorectum | AD | regulation of intracellular transport | 109/3918 | 337/18723 | 5.33e-07 | 1.95e-05 | 109 |
| GO:0043487 | Colorectum | AD | regulation of RNA stability | 63/3918 | 170/18723 | 9.17e-07 | 3.12e-05 | 63 |
| GO:0006403 | Colorectum | AD | RNA localization | 71/3918 | 201/18723 | 1.54e-06 | 4.76e-05 | 71 |
| GO:0051236 | Colorectum | AD | establishment of RNA localization | 58/3918 | 166/18723 | 1.95e-05 | 4.01e-04 | 58 |
| GO:0015931 | Colorectum | AD | nucleobase-containing compound transport | 73/3918 | 222/18723 | 2.02e-05 | 4.10e-04 | 73 |
| GO:0046822 | Colorectum | AD | regulation of nucleocytoplasmic transport | 41/3918 | 106/18723 | 2.17e-05 | 4.33e-04 | 41 |
| GO:0050657 | Colorectum | AD | nucleic acid transport | 57/3918 | 163/18723 | 2.22e-05 | 4.39e-04 | 57 |
| GO:0050658 | Colorectum | AD | RNA transport | 57/3918 | 163/18723 | 2.22e-05 | 4.39e-04 | 57 |
| GO:0001701 | Colorectum | AD | in utero embryonic development | 110/3918 | 367/18723 | 2.36e-05 | 4.62e-04 | 110 |
| GO:0051168 | Colorectum | AD | nuclear export | 53/3918 | 154/18723 | 6.89e-05 | 1.11e-03 | 53 |
| 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 |
| 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 |
| NSUN2 | SNV | Missense_Mutation | c.1876N>A | p.Asp626Asn | p.D626N | Q08J23 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A2-A0CR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR | |
| NSUN2 | SNV | Missense_Mutation | rs745927756 | c.658N>T | p.Arg220Cys | p.R220C | Q08J23 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NSUN2 | SNV | Missense_Mutation | novel | c.2117N>G | p.Val706Gly | p.V706G | Q08J23 | protein_coding | deleterious(0.01) | benign(0.141) | TCGA-AO-A1KP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | SD |
| NSUN2 | SNV | Missense_Mutation | rs759251595 | c.2008N>T | p.Ala670Ser | p.A670S | Q08J23 | protein_coding | tolerated(0.76) | benign(0.02) | TCGA-E9-A2JS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamide | PD |
| NSUN2 | insertion | Nonsense_Mutation | novel | c.1617_1618insTTTCATCTTATTTTTTTACTTACAGGTTATTAACACA | p.Asp540PhefsTer11 | p.D540Ffs*11 | Q08J23 | protein_coding | TCGA-AO-A0J5-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Other, specify in notesBisphosphonate | zoledronic | PD | ||
| NSUN2 | deletion | Frame_Shift_Del | novel | c.403delN | p.Ile135SerfsTer2 | p.I135Sfs*2 | Q08J23 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| NSUN2 | SNV | Missense_Mutation | rs746142475 | c.2167G>A | p.Ala723Thr | p.A723T | Q08J23 | protein_coding | tolerated(0.19) | benign(0.003) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NSUN2 | SNV | Missense_Mutation | novel | c.259G>A | p.Ala87Thr | p.A87T | Q08J23 | protein_coding | deleterious(0.04) | possibly_damaging(0.616) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NSUN2 | SNV | Missense_Mutation | c.178N>A | p.Glu60Lys | p.E60K | Q08J23 | protein_coding | deleterious(0.01) | benign(0.091) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR | |
| NSUN2 | SNV | Missense_Mutation | novel | c.2001N>G | p.Asn667Lys | p.N667K | Q08J23 | protein_coding | tolerated(0.93) | benign(0) | TCGA-VS-A8EK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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 |
| Page: 1 |
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