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Gene: EARS2 |
Gene summary for EARS2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | EARS2 | Gene ID | 124454 |
Gene name | glutamyl-tRNA synthetase 2, mitochondrial | |
Gene Alias | COXPD12 | |
Cytomap | 16p12.2 | |
Gene Type | protein-coding | GO ID | GO:0000959 | UniProtAcc | Q5JPH6 |
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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 |
124454 | EARS2 | LZE2T | Human | Esophagus | ESCC | 4.73e-03 | 2.90e-01 | 0.082 |
124454 | EARS2 | LZE7T | Human | Esophagus | ESCC | 6.33e-03 | 1.59e-01 | 0.0667 |
124454 | EARS2 | LZE24T | Human | Esophagus | ESCC | 1.80e-03 | 9.60e-02 | 0.0596 |
124454 | EARS2 | LZE21T | Human | Esophagus | ESCC | 8.02e-04 | 1.89e-01 | 0.0655 |
124454 | EARS2 | P1T-E | Human | Esophagus | ESCC | 7.11e-04 | 1.86e-01 | 0.0875 |
124454 | EARS2 | P2T-E | Human | Esophagus | ESCC | 1.18e-18 | 3.38e-01 | 0.1177 |
124454 | EARS2 | P4T-E | Human | Esophagus | ESCC | 2.23e-06 | 1.52e-01 | 0.1323 |
124454 | EARS2 | P5T-E | Human | Esophagus | ESCC | 2.43e-06 | 1.38e-01 | 0.1327 |
124454 | EARS2 | P8T-E | Human | Esophagus | ESCC | 6.69e-03 | 8.38e-02 | 0.0889 |
124454 | EARS2 | P9T-E | Human | Esophagus | ESCC | 1.45e-04 | 1.25e-01 | 0.1131 |
124454 | EARS2 | P11T-E | Human | Esophagus | ESCC | 3.25e-05 | 2.05e-01 | 0.1426 |
124454 | EARS2 | P12T-E | Human | Esophagus | ESCC | 1.27e-09 | 2.42e-01 | 0.1122 |
124454 | EARS2 | P15T-E | Human | Esophagus | ESCC | 1.83e-09 | 1.80e-01 | 0.1149 |
124454 | EARS2 | P16T-E | Human | Esophagus | ESCC | 3.90e-14 | 2.40e-01 | 0.1153 |
124454 | EARS2 | P17T-E | Human | Esophagus | ESCC | 1.49e-02 | 1.56e-01 | 0.1278 |
124454 | EARS2 | P20T-E | Human | Esophagus | ESCC | 1.04e-10 | 2.56e-01 | 0.1124 |
124454 | EARS2 | P21T-E | Human | Esophagus | ESCC | 4.90e-09 | 1.99e-01 | 0.1617 |
124454 | EARS2 | P22T-E | Human | Esophagus | ESCC | 1.58e-15 | 1.76e-01 | 0.1236 |
124454 | EARS2 | P23T-E | Human | Esophagus | ESCC | 1.31e-04 | 1.24e-01 | 0.108 |
124454 | EARS2 | P24T-E | Human | Esophagus | ESCC | 8.12e-08 | 2.21e-01 | 0.1287 |
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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. |
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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 |
Breast | Precancer | |
Breast | IDC | |
Breast | DCIS | |
Cervix | CC | |
Cervix | HSIL_HPV |
∗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: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:003254314 | Esophagus | ESCC | mitochondrial translation | 68/8552 | 76/18723 | 1.02e-15 | 6.86e-14 | 68 |
GO:00063992 | Esophagus | ESCC | tRNA metabolic process | 122/8552 | 179/18723 | 9.03e-10 | 2.19e-08 | 122 |
GO:00009592 | Esophagus | ESCC | mitochondrial RNA metabolic process | 39/8552 | 49/18723 | 1.20e-06 | 1.49e-05 | 39 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa012405 | Esophagus | ESCC | Biosynthesis of cofactors | 97/4205 | 153/8465 | 3.88e-04 | 1.35e-03 | 6.94e-04 | 97 |
hsa0124012 | Esophagus | ESCC | Biosynthesis of cofactors | 97/4205 | 153/8465 | 3.88e-04 | 1.35e-03 | 6.94e-04 | 97 |
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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 |
EARS2 | SNV | Missense_Mutation | novel | c.663N>C | p.Lys221Asn | p.K221N | Q5JPH6 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-B6-A400-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
EARS2 | SNV | Missense_Mutation | novel | c.647N>G | p.Asp216Gly | p.D216G | Q5JPH6 | protein_coding | deleterious(0) | possibly_damaging(0.767) | TCGA-C8-A132-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
EARS2 | SNV | Missense_Mutation | novel | c.267G>C | p.Glu89Asp | p.E89D | Q5JPH6 | protein_coding | tolerated(0.11) | benign(0.024) | TCGA-E2-A14V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
EARS2 | insertion | Frame_Shift_Ins | novel | c.260_261insCAGGCAGGAAACACAG | p.Ala88ArgfsTer10 | p.A88Rfs*10 | Q5JPH6 | protein_coding | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
EARS2 | SNV | Missense_Mutation | c.113N>C | p.Arg38Pro | p.R38P | Q5JPH6 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-EK-A2RJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
EARS2 | SNV | Missense_Mutation | novel | c.510N>C | p.Met170Ile | p.M170I | Q5JPH6 | protein_coding | deleterious(0.01) | benign(0.006) | TCGA-PN-A8MA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
EARS2 | SNV | Missense_Mutation | c.910N>T | p.Pro304Ser | p.P304S | Q5JPH6 | protein_coding | deleterious(0.05) | possibly_damaging(0.902) | TCGA-AD-6964-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD | |
EARS2 | SNV | Missense_Mutation | novel | c.1511A>G | p.Asp504Gly | p.D504G | Q5JPH6 | protein_coding | tolerated(0.66) | benign(0) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
EARS2 | SNV | Missense_Mutation | c.1270N>A | p.Leu424Met | p.L424M | Q5JPH6 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-D5-6928-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
EARS2 | SNV | Missense_Mutation | novel | c.1279N>T | p.Arg427Cys | p.R427C | Q5JPH6 | protein_coding | deleterious(0.04) | possibly_damaging(0.448) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
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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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