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Gene: MT1A |
Gene summary for MT1A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MT1A | Gene ID | 4489 |
| Gene name | metallothionein 1A | |
| Gene Alias | MT-1A | |
| Cytomap | 16q13 | |
| Gene Type | protein-coding | GO ID | GO:0006873 | UniProtAcc | P04731 |
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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 |
| 4489 | MT1A | P24T-E | Human | Esophagus | ESCC | 3.31e-04 | -3.88e-02 | 0.1287 |
| 4489 | MT1A | P89T-E | Human | Esophagus | ESCC | 2.23e-10 | 9.58e-01 | 0.1752 |
| 4489 | MT1A | P128T-E | Human | Esophagus | ESCC | 5.34e-15 | 1.29e+00 | 0.1241 |
| 4489 | MT1A | HCC1_Meng | Human | Liver | HCC | 3.31e-68 | 3.07e-01 | 0.0246 |
| 4489 | MT1A | cirrhotic3 | Human | Liver | Cirrhotic | 2.49e-05 | 1.94e-01 | 0.0215 |
| 4489 | MT1A | Pt13.b | Human | Liver | HCC | 4.35e-02 | -1.91e-02 | 0.0251 |
| 4489 | MT1A | S014 | Human | Liver | HCC | 9.15e-07 | 5.79e-01 | 0.2254 |
| 4489 | MT1A | S015 | Human | Liver | HCC | 1.98e-04 | 4.98e-01 | 0.2375 |
| 4489 | MT1A | S016 | Human | Liver | HCC | 2.38e-02 | 3.58e-01 | 0.2243 |
| 4489 | MT1A | S028 | Human | Liver | HCC | 2.53e-07 | 5.46e-01 | 0.2503 |
| 4489 | MT1A | S029 | Human | Liver | HCC | 4.24e-07 | 5.13e-01 | 0.2581 |
| 4489 | MT1A | C04 | Human | Oral cavity | OSCC | 2.13e-06 | -5.28e-01 | 0.2633 |
| 4489 | MT1A | C21 | Human | Oral cavity | OSCC | 2.66e-09 | -9.42e-01 | 0.2678 |
| 4489 | MT1A | C30 | Human | Oral cavity | OSCC | 2.31e-03 | -9.13e-01 | 0.3055 |
| 4489 | MT1A | C43 | Human | Oral cavity | OSCC | 1.58e-19 | -9.49e-01 | 0.1704 |
| 4489 | MT1A | C46 | Human | Oral cavity | OSCC | 4.92e-16 | -9.34e-01 | 0.1673 |
| 4489 | MT1A | C51 | Human | Oral cavity | OSCC | 1.87e-03 | -9.32e-01 | 0.2674 |
| 4489 | MT1A | C57 | Human | Oral cavity | OSCC | 1.07e-12 | -9.52e-01 | 0.1679 |
| 4489 | MT1A | C08 | Human | Oral cavity | OSCC | 2.87e-14 | -8.74e-01 | 0.1919 |
| 4489 | MT1A | C09 | Human | Oral cavity | OSCC | 2.34e-12 | -7.40e-01 | 0.1431 |
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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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:0006575 | Colorectum | AD | cellular modified amino acid metabolic process | 59/3918 | 188/18723 | 4.80e-04 | 5.27e-03 | 59 |
| GO:0042398 | Colorectum | AD | cellular modified amino acid biosynthetic process | 18/3918 | 46/18723 | 3.67e-03 | 2.60e-02 | 18 |
| GO:00423981 | Colorectum | MSS | cellular modified amino acid biosynthetic process | 20/3467 | 46/18723 | 8.26e-05 | 1.35e-03 | 20 |
| GO:00065751 | Colorectum | MSS | cellular modified amino acid metabolic process | 55/3467 | 188/18723 | 2.16e-04 | 3.01e-03 | 55 |
| GO:00459267 | Esophagus | ESCC | negative regulation of growth | 148/8552 | 249/18723 | 7.88e-06 | 7.73e-05 | 148 |
| GO:005507617 | Esophagus | ESCC | transition metal ion homeostasis | 87/8552 | 138/18723 | 2.85e-05 | 2.37e-04 | 87 |
| GO:001003827 | Esophagus | ESCC | response to metal ion | 208/8552 | 373/18723 | 5.02e-05 | 3.90e-04 | 208 |
| GO:004668619 | Esophagus | ESCC | response to cadmium ion | 47/8552 | 68/18723 | 7.81e-05 | 5.80e-04 | 47 |
| GO:000963620 | Esophagus | ESCC | response to toxic substance | 150/8552 | 262/18723 | 1.00e-04 | 7.12e-04 | 150 |
| GO:00469169 | Esophagus | ESCC | cellular transition metal ion homeostasis | 70/8552 | 115/18723 | 7.28e-04 | 3.79e-03 | 70 |
| GO:007124117 | Esophagus | ESCC | cellular response to inorganic substance | 125/8552 | 226/18723 | 2.17e-03 | 9.67e-03 | 125 |
| GO:007127615 | Esophagus | ESCC | cellular response to cadmium ion | 27/8552 | 40/18723 | 4.39e-03 | 1.73e-02 | 27 |
| GO:004668817 | Esophagus | ESCC | response to copper ion | 27/8552 | 42/18723 | 1.16e-02 | 3.90e-02 | 27 |
| GO:001003812 | Liver | Cirrhotic | response to metal ion | 150/4634 | 373/18723 | 2.27e-11 | 1.37e-09 | 150 |
| GO:000963612 | Liver | Cirrhotic | response to toxic substance | 104/4634 | 262/18723 | 5.63e-08 | 1.74e-06 | 104 |
| GO:00550766 | Liver | Cirrhotic | transition metal ion homeostasis | 59/4634 | 138/18723 | 2.59e-06 | 4.65e-05 | 59 |
| GO:004668612 | Liver | Cirrhotic | response to cadmium ion | 34/4634 | 68/18723 | 6.04e-06 | 9.74e-05 | 34 |
| GO:00987547 | Liver | Cirrhotic | detoxification | 60/4634 | 152/18723 | 4.09e-05 | 4.86e-04 | 60 |
| GO:00469164 | Liver | Cirrhotic | cellular transition metal ion homeostasis | 48/4634 | 115/18723 | 4.51e-05 | 5.30e-04 | 48 |
| GO:00712487 | Liver | Cirrhotic | cellular response to metal ion | 73/4634 | 197/18723 | 7.73e-05 | 8.54e-04 | 73 |
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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 |
| MT1A | SNV | Missense_Mutation | novel | c.115A>G | p.Met39Val | p.M39V | P04731 | protein_coding | tolerated(1) | benign(0) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| MT1A | SNV | Missense_Mutation | c.154N>T | p.Gly52Trp | p.G52W | P04731 | protein_coding | deleterious(0) | probably_damaging(0.963) | TCGA-B5-A0JV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| MT1A | SNV | Missense_Mutation | novel | c.165N>T | p.Glu55Asp | p.E55D | P04731 | protein_coding | tolerated(1) | benign(0) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| MT1A | SNV | Missense_Mutation | novel | c.95N>A | p.Ser32Asn | p.S32N | P04731 | protein_coding | tolerated(0.06) | benign(0.239) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| MT1A | SNV | Missense_Mutation | novel | c.110N>T | p.Cys37Phe | p.C37F | P04731 | protein_coding | tolerated(0.05) | probably_damaging(0.997) | TCGA-55-8616-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| MT1A | SNV | Missense_Mutation | novel | c.101N>A | p.Cys34Tyr | p.C34Y | P04731 | protein_coding | deleterious(0.04) | probably_damaging(0.998) | TCGA-43-2581-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| MT1A | SNV | Missense_Mutation | novel | c.22N>A | p.Ala8Thr | p.A8T | P04731 | protein_coding | tolerated(0.45) | benign(0.198) | TCGA-F7-A624-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | 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 |
| 4489 | MT1A | NA | arsenic trioxide | 24924344 | ||
| 4489 | MT1A | NA | oxaliplatin | OXALIPLATIN | 24924344 |
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