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Gene: NSD2 |
Gene summary for NSD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NSD2 | Gene ID | 7468 |
| Gene name | nuclear receptor binding SET domain protein 2 | |
| Gene Alias | KMT3F | |
| Cytomap | 4p16.3 | |
| Gene Type | protein-coding | GO ID | GO:0000018 | UniProtAcc | O96028 |
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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 |
| 7468 | NSD2 | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 8.65e-04 | 2.52e-01 | 0.0208 |
| 7468 | NSD2 | CCI_1 | Human | Cervix | CC | 1.52e-19 | 1.54e+00 | 0.528 |
| 7468 | NSD2 | CCI_2 | Human | Cervix | CC | 1.90e-05 | 7.01e-01 | 0.5249 |
| 7468 | NSD2 | CCI_3 | Human | Cervix | CC | 5.02e-11 | 9.22e-01 | 0.516 |
| 7468 | NSD2 | Tumor | Human | Cervix | CC | 8.11e-04 | -1.47e-01 | 0.1241 |
| 7468 | NSD2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.32e-07 | -3.27e-01 | 0.0155 |
| 7468 | NSD2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.37e-47 | -8.75e-01 | 0.294 |
| 7468 | NSD2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.35e-19 | -8.75e-01 | 0.281 |
| 7468 | NSD2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.75e-49 | -8.75e-01 | 0.3859 |
| 7468 | NSD2 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 6.01e-15 | -8.75e-01 | 0.2585 |
| 7468 | NSD2 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.78e-48 | -8.75e-01 | 0.3005 |
| 7468 | NSD2 | F007 | Human | Colorectum | FAP | 2.40e-02 | -2.62e-01 | 0.1176 |
| 7468 | NSD2 | A002-C-010 | Human | Colorectum | FAP | 1.57e-05 | -2.53e-01 | 0.242 |
| 7468 | NSD2 | A001-C-207 | Human | Colorectum | FAP | 1.13e-02 | -2.44e-01 | 0.1278 |
| 7468 | NSD2 | A015-C-203 | Human | Colorectum | FAP | 1.74e-24 | -3.62e-01 | -0.1294 |
| 7468 | NSD2 | A015-C-204 | Human | Colorectum | FAP | 4.34e-04 | -2.84e-01 | -0.0228 |
| 7468 | NSD2 | A014-C-040 | Human | Colorectum | FAP | 1.23e-03 | -3.59e-01 | -0.1184 |
| 7468 | NSD2 | A002-C-201 | Human | Colorectum | FAP | 5.78e-12 | -3.26e-01 | 0.0324 |
| 7468 | NSD2 | A002-C-203 | Human | Colorectum | FAP | 1.29e-03 | -2.40e-01 | 0.2786 |
| 7468 | NSD2 | A001-C-119 | Human | Colorectum | FAP | 5.77e-06 | 1.46e-01 | -0.1557 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00104525 | Cervix | CC | histone H3-K36 methylation | 8/2311 | 15/18723 | 1.53e-04 | 1.85e-03 | 8 |
| GO:00165705 | Cervix | CC | histone modification | 84/2311 | 463/18723 | 1.70e-04 | 2.01e-03 | 84 |
| GO:20010209 | Cervix | CC | regulation of response to DNA damage stimulus | 46/2311 | 219/18723 | 1.92e-04 | 2.23e-03 | 46 |
| GO:00349685 | Cervix | CC | histone lysine methylation | 27/2311 | 115/18723 | 6.61e-04 | 6.09e-03 | 27 |
| GO:00026973 | Cervix | CC | regulation of immune effector process | 62/2311 | 339/18723 | 9.25e-04 | 7.84e-03 | 62 |
| GO:00510528 | Cervix | CC | regulation of DNA metabolic process | 65/2311 | 359/18723 | 9.25e-04 | 7.84e-03 | 65 |
| GO:00026967 | Cervix | CC | positive regulation of leukocyte activation | 72/2311 | 409/18723 | 1.13e-03 | 9.31e-03 | 72 |
| GO:00512516 | Cervix | CC | positive regulation of lymphocyte activation | 65/2311 | 362/18723 | 1.15e-03 | 9.39e-03 | 65 |
| GO:00508676 | Cervix | CC | positive regulation of cell activation | 73/2311 | 420/18723 | 1.50e-03 | 1.16e-02 | 73 |
| GO:00165715 | Cervix | CC | histone methylation | 30/2311 | 141/18723 | 1.88e-03 | 1.39e-02 | 30 |
| GO:00180224 | Cervix | CC | peptidyl-lysine methylation | 28/2311 | 131/18723 | 2.43e-03 | 1.71e-02 | 28 |
| GO:00064795 | Cervix | CC | protein methylation | 36/2311 | 181/18723 | 2.46e-03 | 1.71e-02 | 36 |
| GO:00082135 | Cervix | CC | protein alkylation | 36/2311 | 181/18723 | 2.46e-03 | 1.71e-02 | 36 |
| GO:00024603 | Cervix | CC | adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 62/2311 | 356/18723 | 3.09e-03 | 2.03e-02 | 62 |
| GO:0002263 | Cervix | CC | cell activation involved in immune response | 50/2311 | 279/18723 | 4.16e-03 | 2.57e-02 | 50 |
| GO:0002443 | Cervix | CC | leukocyte mediated immunity | 73/2311 | 440/18723 | 5.01e-03 | 2.98e-02 | 73 |
| GO:0002699 | Cervix | CC | positive regulation of immune effector process | 43/2311 | 235/18723 | 5.13e-03 | 3.02e-02 | 43 |
| GO:0002819 | Cervix | CC | regulation of adaptive immune response | 35/2311 | 183/18723 | 5.38e-03 | 3.11e-02 | 35 |
| GO:0002822 | Cervix | CC | regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | 32/2311 | 168/18723 | 8.00e-03 | 4.18e-02 | 32 |
| GO:00023813 | Cervix | CC | immunoglobulin production involved in immunoglobulin-mediated immune response | 16/2311 | 70/18723 | 1.01e-02 | 4.91e-02 | 16 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa00310 | Colorectum | AD | Lysine degradation | 27/2092 | 63/8465 | 1.17e-03 | 7.75e-03 | 4.94e-03 | 27 |
| hsa003101 | Colorectum | AD | Lysine degradation | 27/2092 | 63/8465 | 1.17e-03 | 7.75e-03 | 4.94e-03 | 27 |
| hsa003102 | Colorectum | MSS | Lysine degradation | 24/1875 | 63/8465 | 2.94e-03 | 1.39e-02 | 8.50e-03 | 24 |
| hsa003103 | Colorectum | MSS | Lysine degradation | 24/1875 | 63/8465 | 2.94e-03 | 1.39e-02 | 8.50e-03 | 24 |
| hsa003104 | Colorectum | FAP | Lysine degradation | 23/1404 | 63/8465 | 1.04e-04 | 9.46e-04 | 5.76e-04 | 23 |
| hsa05202 | Colorectum | FAP | Transcriptional misregulation in cancer | 45/1404 | 193/8465 | 9.19e-03 | 3.33e-02 | 2.03e-02 | 45 |
| hsa003105 | Colorectum | FAP | Lysine degradation | 23/1404 | 63/8465 | 1.04e-04 | 9.46e-04 | 5.76e-04 | 23 |
| hsa052021 | Colorectum | FAP | Transcriptional misregulation in cancer | 45/1404 | 193/8465 | 9.19e-03 | 3.33e-02 | 2.03e-02 | 45 |
| hsa003106 | Colorectum | CRC | Lysine degradation | 18/1091 | 63/8465 | 7.21e-04 | 6.34e-03 | 4.30e-03 | 18 |
| hsa003107 | Colorectum | CRC | Lysine degradation | 18/1091 | 63/8465 | 7.21e-04 | 6.34e-03 | 4.30e-03 | 18 |
| hsa052026 | Lung | IAC | Transcriptional misregulation in cancer | 40/1053 | 193/8465 | 6.90e-04 | 5.90e-03 | 3.92e-03 | 40 |
| hsa003109 | Lung | IAC | Lysine degradation | 17/1053 | 63/8465 | 1.35e-03 | 8.63e-03 | 5.73e-03 | 17 |
| hsa0520211 | Lung | IAC | Transcriptional misregulation in cancer | 40/1053 | 193/8465 | 6.90e-04 | 5.90e-03 | 3.92e-03 | 40 |
| hsa0031012 | Lung | IAC | Lysine degradation | 17/1053 | 63/8465 | 1.35e-03 | 8.63e-03 | 5.73e-03 | 17 |
| hsa052022 | Lung | AIS | Transcriptional misregulation in cancer | 39/961 | 193/8465 | 2.15e-04 | 2.41e-03 | 1.54e-03 | 39 |
| hsa0031022 | Lung | AIS | Lysine degradation | 16/961 | 63/8465 | 1.41e-03 | 9.49e-03 | 6.07e-03 | 16 |
| hsa052023 | Lung | AIS | Transcriptional misregulation in cancer | 39/961 | 193/8465 | 2.15e-04 | 2.41e-03 | 1.54e-03 | 39 |
| hsa0031032 | Lung | AIS | Lysine degradation | 16/961 | 63/8465 | 1.41e-03 | 9.49e-03 | 6.07e-03 | 16 |
| hsa052024 | Lung | MIAC | Transcriptional misregulation in cancer | 22/507 | 193/8465 | 2.64e-03 | 2.26e-02 | 1.64e-02 | 22 |
| hsa0031042 | Lung | MIAC | Lysine degradation | 10/507 | 63/8465 | 3.93e-03 | 3.18e-02 | 2.30e-02 | 10 |
| 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 |
| 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 |
| NSD2 | SNV | Missense_Mutation | c.1289A>G | p.Asp430Gly | p.D430G | O96028 | protein_coding | tolerated(0.13) | benign(0.036) | TCGA-A8-A06R-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| NSD2 | SNV | Missense_Mutation | c.1656N>G | p.Asp552Glu | p.D552E | O96028 | protein_coding | tolerated(0.53) | benign(0.003) | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | |
| NSD2 | SNV | Missense_Mutation | rs772470710 | c.3295G>A | p.Glu1099Lys | p.E1099K | O96028 | protein_coding | deleterious(0) | probably_damaging(0.949) | TCGA-AR-A0TT-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD |
| NSD2 | SNV | Missense_Mutation | c.1777N>A | p.Ala593Thr | p.A593T | O96028 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-B6-A0I6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| NSD2 | SNV | Missense_Mutation | c.3502N>A | p.Asp1168Asn | p.D1168N | O96028 | protein_coding | tolerated(0.05) | probably_damaging(0.998) | TCGA-E2-A10C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| NSD2 | insertion | Frame_Shift_Ins | novel | c.3556_3557insTGCTGACCTTAGCTCCCTTGTTTGCCATC | p.Asn1186MetfsTer153 | p.N1186Mfs*153 | O96028 | protein_coding | TCGA-B6-A0I6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | ||
| NSD2 | deletion | Frame_Shift_Del | novel | c.201delN | p.His68ThrfsTer12 | p.H68Tfs*12 | O96028 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| NSD2 | SNV | Missense_Mutation | rs753748334 | c.208G>A | p.Ala70Thr | p.A70T | O96028 | protein_coding | tolerated(0.32) | benign(0.005) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NSD2 | SNV | Missense_Mutation | novel | c.844G>A | p.Val282Ile | p.V282I | O96028 | protein_coding | deleterious(0.02) | probably_damaging(0.965) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| NSD2 | SNV | Missense_Mutation | novel | c.1814C>T | p.Thr605Met | p.T605M | O96028 | protein_coding | deleterious(0.02) | benign(0.231) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
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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 |
| 7468 | NSD2 | CLINICALLY ACTIONABLE, METHYL TRANSFERASE, ENZYME | NSC-36398 | CHEMBL483206 | ||
| 7468 | NSD2 | CLINICALLY ACTIONABLE, METHYL TRANSFERASE, ENZYME | MITOXANTRONE | MITOXANTRONE | ||
| 7468 | NSD2 | CLINICALLY ACTIONABLE, METHYL TRANSFERASE, ENZYME | 4-AMINO-[1,2]NAPHTHOQUINONE | 4-AMINO-[1,2]NAPHTHOQUINONE | ||
| 7468 | NSD2 | CLINICALLY ACTIONABLE, METHYL TRANSFERASE, ENZYME | NSC-228155 | CHEMBL505670 | ||
| 7468 | NSD2 | CLINICALLY ACTIONABLE, METHYL TRANSFERASE, ENZYME | DNDI1416917 | CHEMBL1335833 | ||
| 7468 | NSD2 | CLINICALLY ACTIONABLE, METHYL TRANSFERASE, ENZYME | GNF-PF-4459 | CHEMBL585502 | ||
| 7468 | NSD2 | CLINICALLY ACTIONABLE, METHYL TRANSFERASE, ENZYME | N-(4-CARBOXYMETHENE)PHENYLPYRROLE | CHEMBL258756 | ||
| 7468 | NSD2 | CLINICALLY ACTIONABLE, METHYL TRANSFERASE, ENZYME | ACID BLUE 129 | ACID BLUE 129 | ||
| 7468 | NSD2 | CLINICALLY ACTIONABLE, METHYL TRANSFERASE, ENZYME | GNF-PF-5159 | CHEMBL1493528 | ||
| 7468 | NSD2 | CLINICALLY ACTIONABLE, METHYL TRANSFERASE, ENZYME | PURPUROGALLIN | PURPUROGALLIN |
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