|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: NSUN3 |
Gene summary for NSUN3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NSUN3 | Gene ID | 63899 |
| Gene name | NOP2/Sun RNA methyltransferase 3 | |
| Gene Alias | COXPD48 | |
| Cytomap | 3q11.2 | |
| Gene Type | protein-coding | GO ID | GO:0000154 | UniProtAcc | Q9H649 |
Top |
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 |
| 63899 | NSUN3 | LZE4T | Human | Esophagus | ESCC | 1.61e-09 | 2.65e-01 | 0.0811 |
| 63899 | NSUN3 | LZE8T | Human | Esophagus | ESCC | 8.05e-03 | 1.17e-01 | 0.067 |
| 63899 | NSUN3 | LZE24T | Human | Esophagus | ESCC | 2.98e-09 | 2.57e-01 | 0.0596 |
| 63899 | NSUN3 | P1T-E | Human | Esophagus | ESCC | 1.78e-02 | 1.50e-01 | 0.0875 |
| 63899 | NSUN3 | P2T-E | Human | Esophagus | ESCC | 1.37e-06 | 1.28e-01 | 0.1177 |
| 63899 | NSUN3 | P4T-E | Human | Esophagus | ESCC | 2.47e-31 | 5.74e-01 | 0.1323 |
| 63899 | NSUN3 | P5T-E | Human | Esophagus | ESCC | 3.13e-07 | 1.37e-01 | 0.1327 |
| 63899 | NSUN3 | P8T-E | Human | Esophagus | ESCC | 3.41e-13 | 2.37e-01 | 0.0889 |
| 63899 | NSUN3 | P9T-E | Human | Esophagus | ESCC | 2.10e-11 | 1.99e-01 | 0.1131 |
| 63899 | NSUN3 | P10T-E | Human | Esophagus | ESCC | 1.02e-18 | 3.20e-01 | 0.116 |
| 63899 | NSUN3 | P11T-E | Human | Esophagus | ESCC | 1.79e-09 | 3.47e-01 | 0.1426 |
| 63899 | NSUN3 | P12T-E | Human | Esophagus | ESCC | 1.82e-03 | 9.26e-02 | 0.1122 |
| 63899 | NSUN3 | P15T-E | Human | Esophagus | ESCC | 2.75e-04 | 1.19e-01 | 0.1149 |
| 63899 | NSUN3 | P16T-E | Human | Esophagus | ESCC | 1.15e-13 | 1.82e-01 | 0.1153 |
| 63899 | NSUN3 | P20T-E | Human | Esophagus | ESCC | 3.39e-08 | 1.74e-01 | 0.1124 |
| 63899 | NSUN3 | P21T-E | Human | Esophagus | ESCC | 1.27e-08 | 1.31e-01 | 0.1617 |
| 63899 | NSUN3 | P22T-E | Human | Esophagus | ESCC | 2.32e-07 | 1.58e-01 | 0.1236 |
| 63899 | NSUN3 | P23T-E | Human | Esophagus | ESCC | 3.50e-06 | 1.63e-01 | 0.108 |
| 63899 | NSUN3 | P24T-E | Human | Esophagus | ESCC | 3.92e-03 | 1.37e-01 | 0.1287 |
| 63899 | NSUN3 | P26T-E | Human | Esophagus | ESCC | 2.54e-10 | 2.18e-01 | 0.1276 |
| Page: 1 2 3 |
| 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 |
| ∗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. |
Top |
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:014005313 | Esophagus | ESCC | mitochondrial gene expression | 93/8552 | 108/18723 | 1.96e-18 | 2.03e-16 | 93 |
| GO:0006417111 | Esophagus | ESCC | regulation of translation | 304/8552 | 468/18723 | 1.53e-17 | 1.33e-15 | 304 |
| GO:003254314 | Esophagus | ESCC | mitochondrial translation | 68/8552 | 76/18723 | 1.02e-15 | 6.86e-14 | 68 |
| GO:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
| GO:00080333 | Esophagus | ESCC | tRNA processing | 92/8552 | 127/18723 | 7.83e-10 | 1.93e-08 | 92 |
| GO:00063992 | Esophagus | ESCC | tRNA metabolic process | 122/8552 | 179/18723 | 9.03e-10 | 2.19e-08 | 122 |
| 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:00701292 | Esophagus | ESCC | regulation of mitochondrial translation | 22/8552 | 24/18723 | 2.82e-06 | 3.21e-05 | 22 |
| GO:00015101 | Esophagus | ESCC | RNA methylation | 58/8552 | 83/18723 | 6.87e-06 | 6.94e-05 | 58 |
| GO:00064002 | Esophagus | ESCC | tRNA modification | 62/8552 | 90/18723 | 7.02e-06 | 7.04e-05 | 62 |
| GO:00621252 | Esophagus | ESCC | regulation of mitochondrial gene expression | 24/8552 | 28/18723 | 1.37e-05 | 1.25e-04 | 24 |
| GO:00304881 | Esophagus | ESCC | tRNA methylation | 30/8552 | 41/18723 | 3.27e-04 | 1.93e-03 | 30 |
| GO:0000154 | Esophagus | ESCC | rRNA modification | 26/8552 | 37/18723 | 2.16e-03 | 9.62e-03 | 26 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| NSUN3 | SNV | Missense_Mutation | c.900C>G | p.His300Gln | p.H300Q | Q9H649 | protein_coding | tolerated(1) | benign(0) | TCGA-AR-A1AH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | PD | ||
| NSUN3 | SNV | Missense_Mutation | c.952N>C | p.Asp318His | p.D318H | Q9H649 | protein_coding | tolerated(0.55) | benign(0.009) | TCGA-AR-A255-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | trastuzumab | SD | |
| NSUN3 | SNV | Missense_Mutation | c.504G>C | p.Leu168Phe | p.L168F | Q9H649 | protein_coding | tolerated(0.71) | benign(0.005) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| NSUN3 | SNV | Missense_Mutation | c.676N>C | p.Ser226Pro | p.S226P | Q9H649 | protein_coding | tolerated(0.28) | benign(0.018) | TCGA-AY-A54L-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| NSUN3 | SNV | Missense_Mutation | c.767N>T | p.Pro256Leu | p.P256L | Q9H649 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| NSUN3 | SNV | Missense_Mutation | rs757503445 | c.638C>T | p.Pro213Leu | p.P213L | Q9H649 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| NSUN3 | SNV | Missense_Mutation | c.617N>G | p.Asp206Gly | p.D206G | Q9H649 | protein_coding | deleterious(0) | probably_damaging(0.926) | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR | |
| NSUN3 | SNV | Missense_Mutation | c.145T>G | p.Cys49Gly | p.C49G | Q9H649 | protein_coding | deleterious(0.03) | benign(0.015) | TCGA-AG-3883-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| NSUN3 | SNV | Missense_Mutation | novel | c.232N>A | p.Ser78Thr | p.S78T | Q9H649 | protein_coding | tolerated(0.57) | benign(0.012) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| NSUN3 | SNV | Missense_Mutation | novel | c.565N>T | p.Val189Leu | p.V189L | Q9H649 | protein_coding | tolerated(0.06) | benign(0.286) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |