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Gene: VARS2 |
Gene summary for VARS2 |
Gene summary. |
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 |
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 |
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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Transcriptomic changes along malignancy continuum. |
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 |
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 |
Liver | Cyst | |
Lung | IAC | |
Lung | AIS | |
Lung | AAH | |
Lung | MIAC |
∗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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Enriched GO biological processes. |
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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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
VARS2 | SNV | Missense_Mutation | novel | c.1684N>G | p.Gln562Glu | p.Q562E | Q5ST30 | protein_coding | deleterious(0) | benign(0.062) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
VARS2 | SNV | Missense_Mutation | novel | c.107N>A | p.Leu36His | p.L36H | Q5ST30 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.826) | TCGA-A2-A0T2-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | xeloda | PD |
VARS2 | SNV | Missense_Mutation | c.506N>G | p.Phe169Cys | p.F169C | Q5ST30 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-BH-A0BV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | SD | |
VARS2 | SNV | Missense_Mutation | rs374148426 | c.953N>T | p.Ser318Leu | p.S318L | Q5ST30 | protein_coding | deleterious(0.01) | probably_damaging(0.988) | TCGA-BH-A1EV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
VARS2 | insertion | Frame_Shift_Ins | novel | c.1000_1001insAGTCACA | p.Arg334GlnfsTer28 | p.R334Qfs*28 | Q5ST30 | protein_coding | TCGA-A8-A06Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | PD | ||
VARS2 | insertion | Frame_Shift_Ins | novel | c.984_985insTGTA | p.Gly329CysfsTer32 | p.G329Cfs*32 | Q5ST30 | protein_coding | TCGA-AO-A03L-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
VARS2 | insertion | In_Frame_Ins | novel | c.708_709insGTTAGTATCTGGCAGGGAGGGGTCCTAAATTGTCTC | p.Arg236_His237insValSerIleTrpGlnGlyGlyValLeuAsnCysLeu | p.R236_H237insVSIWQGGVLNCL | Q5ST30 | protein_coding | TCGA-BH-A0HY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | taxotere | CR | ||
VARS2 | deletion | Frame_Shift_Del | novel | c.469delN | p.Tyr157IlefsTer78 | p.Y157Ifs*78 | Q5ST30 | protein_coding | TCGA-E2-A15A-06 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
VARS2 | SNV | Missense_Mutation | novel | c.239G>A | p.Arg80His | p.R80H | Q5ST30 | protein_coding | deleterious(0) | probably_damaging(0.982) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
VARS2 | SNV | Missense_Mutation | rs183132980 | c.2420C>T | p.Pro807Leu | p.P807L | Q5ST30 | protein_coding | tolerated(0.67) | benign(0.003) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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 |
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