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Gene: NSUN4 |
Gene summary for NSUN4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NSUN4 | Gene ID | 387338 |
| Gene name | NOP2/Sun RNA methyltransferase 4 | |
| Gene Alias | SHTAP | |
| Cytomap | 1p33 | |
| Gene Type | protein-coding | GO ID | GO:0000154 | UniProtAcc | Q96CB9 |
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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 |
| 387338 | NSUN4 | LZE7T | Human | Esophagus | ESCC | 2.90e-05 | 1.72e-01 | 0.0667 |
| 387338 | NSUN4 | LZE20T | Human | Esophagus | ESCC | 1.67e-04 | 1.42e-01 | 0.0662 |
| 387338 | NSUN4 | LZE24T | Human | Esophagus | ESCC | 1.42e-09 | 2.40e-01 | 0.0596 |
| 387338 | NSUN4 | P1T-E | Human | Esophagus | ESCC | 1.62e-02 | 2.01e-01 | 0.0875 |
| 387338 | NSUN4 | P2T-E | Human | Esophagus | ESCC | 2.97e-16 | 3.37e-01 | 0.1177 |
| 387338 | NSUN4 | P4T-E | Human | Esophagus | ESCC | 7.79e-10 | 2.02e-01 | 0.1323 |
| 387338 | NSUN4 | P5T-E | Human | Esophagus | ESCC | 2.24e-05 | 1.20e-01 | 0.1327 |
| 387338 | NSUN4 | P8T-E | Human | Esophagus | ESCC | 1.93e-13 | 1.04e-01 | 0.0889 |
| 387338 | NSUN4 | P9T-E | Human | Esophagus | ESCC | 1.72e-07 | 1.38e-01 | 0.1131 |
| 387338 | NSUN4 | P10T-E | Human | Esophagus | ESCC | 2.74e-18 | 3.07e-01 | 0.116 |
| 387338 | NSUN4 | P11T-E | Human | Esophagus | ESCC | 8.40e-04 | 1.89e-01 | 0.1426 |
| 387338 | NSUN4 | P12T-E | Human | Esophagus | ESCC | 1.03e-07 | 1.77e-01 | 0.1122 |
| 387338 | NSUN4 | P15T-E | Human | Esophagus | ESCC | 9.78e-12 | 2.74e-01 | 0.1149 |
| 387338 | NSUN4 | P16T-E | Human | Esophagus | ESCC | 9.27e-10 | 1.45e-01 | 0.1153 |
| 387338 | NSUN4 | P17T-E | Human | Esophagus | ESCC | 1.88e-07 | 2.23e-01 | 0.1278 |
| 387338 | NSUN4 | P20T-E | Human | Esophagus | ESCC | 1.58e-15 | 2.20e-01 | 0.1124 |
| 387338 | NSUN4 | P21T-E | Human | Esophagus | ESCC | 7.32e-17 | 2.94e-01 | 0.1617 |
| 387338 | NSUN4 | P22T-E | Human | Esophagus | ESCC | 1.96e-05 | 9.26e-02 | 0.1236 |
| 387338 | NSUN4 | P23T-E | Human | Esophagus | ESCC | 4.07e-18 | 4.94e-01 | 0.108 |
| 387338 | NSUN4 | P24T-E | Human | Esophagus | ESCC | 2.56e-08 | 9.87e-02 | 0.1287 |
| Page: 1 2 3 4 |
| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0042254111 | Esophagus | ESCC | ribosome biogenesis | 252/8552 | 299/18723 | 3.27e-44 | 1.04e-40 | 252 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:0006364110 | Esophagus | ESCC | rRNA processing | 189/8552 | 225/18723 | 4.88e-33 | 3.87e-30 | 189 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
| GO:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
| GO:00094512 | Esophagus | ESCC | RNA modification | 114/8552 | 167/18723 | 2.76e-09 | 6.04e-08 | 114 |
| GO:00015101 | Esophagus | ESCC | RNA methylation | 58/8552 | 83/18723 | 6.87e-06 | 6.94e-05 | 58 |
| GO:0000154 | Esophagus | ESCC | rRNA modification | 26/8552 | 37/18723 | 2.16e-03 | 9.62e-03 | 26 |
| GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
| GO:004225422 | Liver | HCC | ribosome biogenesis | 246/7958 | 299/18723 | 4.99e-46 | 1.58e-42 | 246 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| GO:001607212 | Liver | HCC | rRNA metabolic process | 193/7958 | 236/18723 | 1.26e-35 | 1.14e-32 | 193 |
| GO:000636421 | Liver | HCC | rRNA processing | 185/7958 | 225/18723 | 8.14e-35 | 6.45e-32 | 185 |
| GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
| GO:00434141 | Liver | HCC | macromolecule methylation | 183/7958 | 316/18723 | 2.00e-08 | 4.72e-07 | 183 |
| GO:0032259 | Liver | HCC | methylation | 206/7958 | 364/18723 | 3.35e-08 | 7.53e-07 | 206 |
| GO:0009451 | Liver | HCC | RNA modification | 101/7958 | 167/18723 | 2.02e-06 | 2.78e-05 | 101 |
| Page: 1 2 |
| 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 |
| NSUN4 | SNV | Missense_Mutation | c.688N>G | p.Gln230Glu | p.Q230E | Q96CB9 | protein_coding | tolerated(0.38) | benign(0.003) | TCGA-AO-A0J6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| NSUN4 | SNV | Missense_Mutation | c.799N>A | p.Glu267Lys | p.E267K | Q96CB9 | protein_coding | deleterious(0.01) | possibly_damaging(0.475) | TCGA-EK-A2R8-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| NSUN4 | SNV | Missense_Mutation | c.334N>T | p.Gly112Cys | p.G112C | Q96CB9 | protein_coding | deleterious(0.02) | possibly_damaging(0.552) | TCGA-A6-3809-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NSUN4 | SNV | Missense_Mutation | c.994N>C | p.Tyr332His | p.Y332H | Q96CB9 | protein_coding | tolerated(0.87) | benign(0.01) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| NSUN4 | SNV | Missense_Mutation | c.349N>A | p.Ala117Thr | p.A117T | Q96CB9 | protein_coding | tolerated(0.61) | benign(0.001) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NSUN4 | SNV | Missense_Mutation | c.971C>A | p.Ala324Asp | p.A324D | Q96CB9 | protein_coding | deleterious(0) | possibly_damaging(0.846) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NSUN4 | SNV | Missense_Mutation | c.135N>C | p.Leu45Phe | p.L45F | Q96CB9 | protein_coding | deleterious(0.01) | probably_damaging(0.976) | TCGA-AG-A025-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NSUN4 | SNV | Missense_Mutation | novel | c.880N>A | p.Ala294Thr | p.A294T | Q96CB9 | protein_coding | deleterious(0.01) | benign(0.326) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| NSUN4 | SNV | Missense_Mutation | rs201711075 | c.785N>A | p.Arg262His | p.R262H | Q96CB9 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AX-A0J1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NSUN4 | SNV | Missense_Mutation | novel | c.683G>A | p.Gly228Glu | p.G228E | Q96CB9 | protein_coding | tolerated(1) | benign(0.001) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| Page: 1 2 3 |
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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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