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Gene: VARS2 |
Gene summary for VARS2 |
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Gene information | Species | Human | Gene symbol | VARS2 | Gene ID | 57176 |
Gene name | valyl-tRNA synthetase 2, mitochondrial | |
Gene Alias | COXPD20 | |
Cytomap | 6p21.33 | |
Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | B4E0K6 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
57176 | VARS2 | HCC1_Meng | Human | Liver | HCC | 4.82e-28 | 4.47e-02 | 0.0246 |
57176 | VARS2 | HCC1 | Human | Liver | HCC | 3.47e-03 | 2.54e+00 | 0.5336 |
57176 | VARS2 | HCC2 | Human | Liver | HCC | 4.29e-13 | 3.64e+00 | 0.5341 |
57176 | VARS2 | S028 | Human | Liver | HCC | 6.34e-05 | 2.80e-01 | 0.2503 |
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Tissue | Expression Dynamics | Abbreviation |
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 |
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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). |
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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
GO:00065202 | Liver | HCC | cellular amino acid metabolic process | 167/7958 | 284/18723 | 1.91e-08 | 4.56e-07 | 167 |
GO:0006399 | Liver | HCC | tRNA metabolic process | 108/7958 | 179/18723 | 1.07e-06 | 1.59e-05 | 108 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
VARS2 | SNV | Missense_Mutation | novel | c.322C>T | p.Pro108Ser | p.P108S | Q5ST30 | protein_coding | tolerated(0.12) | benign(0.031) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VARS2 | SNV | Missense_Mutation | novel | c.3259G>A | p.Ala1087Thr | p.A1087T | Q5ST30 | protein_coding | tolerated_low_confidence(0.39) | benign(0.01) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VARS2 | SNV | Missense_Mutation | rs150863068 | c.541N>C | p.Ser181Pro | p.S181P | Q5ST30 | protein_coding | deleterious(0) | possibly_damaging(0.576) | TCGA-BG-A0MQ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
VARS2 | SNV | Missense_Mutation | c.2351N>A | p.Arg784His | p.R784H | Q5ST30 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-BG-A220-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
VARS2 | SNV | Missense_Mutation | novel | c.188N>G | p.Glu63Gly | p.E63G | Q5ST30 | protein_coding | deleterious(0.03) | benign(0.003) | TCGA-BG-A3EW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
VARS2 | SNV | Missense_Mutation | novel | c.928T>A | p.Ser310Thr | p.S310T | Q5ST30 | protein_coding | deleterious(0.02) | probably_damaging(0.988) | TCGA-BS-A0UL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VARS2 | SNV | Missense_Mutation | rs368986102 | c.1580N>T | p.Ser527Leu | p.S527L | Q5ST30 | protein_coding | tolerated(0.07) | possibly_damaging(0.827) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
VARS2 | SNV | Missense_Mutation | novel | c.991N>G | p.Thr331Ala | p.T331A | Q5ST30 | protein_coding | deleterious(0) | possibly_damaging(0.793) | TCGA-DI-A1BU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
VARS2 | SNV | Missense_Mutation | rs751661981 | c.2281N>A | p.Asp761Asn | p.D761N | Q5ST30 | protein_coding | deleterious(0.03) | benign(0.023) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
VARS2 | SNV | Missense_Mutation | rs370284242 | c.2276N>T | p.Ala759Val | p.A759V | Q5ST30 | protein_coding | deleterious(0.01) | benign(0.029) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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