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Gene: MIA3 |
Gene summary for MIA3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MIA3 | Gene ID | 375056 |
| Gene name | MIA SH3 domain ER export factor 3 | |
| Gene Alias | ARNT | |
| Cytomap | 1q41 | |
| Gene Type | protein-coding | GO ID | GO:0001525 | UniProtAcc | Q5JRA6 |
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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 |
| 375056 | MIA3 | LZE2T | Human | Esophagus | ESCC | 5.15e-10 | 6.99e-01 | 0.082 |
| 375056 | MIA3 | LZE4T | Human | Esophagus | ESCC | 5.61e-15 | 4.75e-01 | 0.0811 |
| 375056 | MIA3 | LZE5T | Human | Esophagus | ESCC | 3.25e-05 | 5.34e-01 | 0.0514 |
| 375056 | MIA3 | LZE7T | Human | Esophagus | ESCC | 7.83e-12 | 6.69e-01 | 0.0667 |
| 375056 | MIA3 | LZE20T | Human | Esophagus | ESCC | 7.03e-08 | 2.04e-01 | 0.0662 |
| 375056 | MIA3 | LZE22D1 | Human | Esophagus | HGIN | 6.09e-03 | 8.30e-02 | 0.0595 |
| 375056 | MIA3 | LZE22T | Human | Esophagus | ESCC | 1.58e-05 | 5.56e-01 | 0.068 |
| 375056 | MIA3 | LZE24T | Human | Esophagus | ESCC | 1.06e-21 | 6.70e-01 | 0.0596 |
| 375056 | MIA3 | LZE6T | Human | Esophagus | ESCC | 4.92e-03 | 2.37e-01 | 0.0845 |
| 375056 | MIA3 | P1T-E | Human | Esophagus | ESCC | 2.91e-20 | 7.80e-01 | 0.0875 |
| 375056 | MIA3 | P2T-E | Human | Esophagus | ESCC | 1.37e-44 | 8.44e-01 | 0.1177 |
| 375056 | MIA3 | P4T-E | Human | Esophagus | ESCC | 1.47e-11 | 3.95e-01 | 0.1323 |
| 375056 | MIA3 | P5T-E | Human | Esophagus | ESCC | 2.35e-20 | 3.02e-01 | 0.1327 |
| 375056 | MIA3 | P8T-E | Human | Esophagus | ESCC | 1.32e-23 | 4.53e-01 | 0.0889 |
| 375056 | MIA3 | P9T-E | Human | Esophagus | ESCC | 6.11e-15 | 3.93e-01 | 0.1131 |
| 375056 | MIA3 | P10T-E | Human | Esophagus | ESCC | 1.90e-30 | 5.58e-01 | 0.116 |
| 375056 | MIA3 | P11T-E | Human | Esophagus | ESCC | 4.21e-19 | 6.70e-01 | 0.1426 |
| 375056 | MIA3 | P12T-E | Human | Esophagus | ESCC | 1.13e-18 | 3.74e-01 | 0.1122 |
| 375056 | MIA3 | P15T-E | Human | Esophagus | ESCC | 1.79e-23 | 5.28e-01 | 0.1149 |
| 375056 | MIA3 | P16T-E | Human | Esophagus | ESCC | 3.00e-24 | 5.53e-01 | 0.1153 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:004819317 | Esophagus | HGIN | Golgi vesicle transport | 83/2587 | 296/18723 | 8.59e-11 | 8.89e-09 | 83 |
| GO:00068889 | Esophagus | HGIN | endoplasmic reticulum to Golgi vesicle-mediated transport | 40/2587 | 130/18723 | 4.67e-07 | 2.07e-05 | 40 |
| GO:000690020 | Esophagus | HGIN | vesicle budding from membrane | 23/2587 | 61/18723 | 2.85e-06 | 9.93e-05 | 23 |
| GO:007097210 | Esophagus | HGIN | protein localization to endoplasmic reticulum | 26/2587 | 74/18723 | 3.09e-06 | 1.05e-04 | 26 |
| GO:00160509 | Esophagus | HGIN | vesicle organization | 65/2587 | 300/18723 | 1.24e-04 | 2.54e-03 | 65 |
| GO:00901146 | Esophagus | HGIN | COPII-coated vesicle budding | 11/2587 | 29/18723 | 1.08e-03 | 1.32e-02 | 11 |
| GO:00070295 | Esophagus | HGIN | endoplasmic reticulum organization | 22/2587 | 87/18723 | 3.07e-03 | 2.90e-02 | 22 |
| GO:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
| GO:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
| GO:000688815 | Esophagus | ESCC | endoplasmic reticulum to Golgi vesicle-mediated transport | 102/8552 | 130/18723 | 1.73e-14 | 9.22e-13 | 102 |
| GO:0006900111 | Esophagus | ESCC | vesicle budding from membrane | 54/8552 | 61/18723 | 2.66e-12 | 1.07e-10 | 54 |
| GO:000702914 | Esophagus | ESCC | endoplasmic reticulum organization | 65/8552 | 87/18723 | 3.28e-08 | 6.08e-07 | 65 |
| GO:009011414 | Esophagus | ESCC | COPII-coated vesicle budding | 27/8552 | 29/18723 | 8.09e-08 | 1.39e-06 | 27 |
| GO:004206027 | Esophagus | ESCC | wound healing | 243/8552 | 422/18723 | 4.62e-07 | 6.25e-06 | 243 |
| GO:007097218 | Esophagus | ESCC | protein localization to endoplasmic reticulum | 52/8552 | 74/18723 | 1.58e-05 | 1.42e-04 | 52 |
| GO:00901104 | Esophagus | ESCC | COPII-coated vesicle cargo loading | 14/8552 | 15/18723 | 1.47e-04 | 9.85e-04 | 14 |
| GO:002240720 | Esophagus | ESCC | regulation of cell-cell adhesion | 239/8552 | 448/18723 | 5.88e-04 | 3.19e-03 | 239 |
| GO:000268316 | Esophagus | ESCC | negative regulation of immune system process | 231/8552 | 434/18723 | 8.48e-04 | 4.36e-03 | 231 |
| GO:000166720 | Esophagus | ESCC | ameboidal-type cell migration | 250/8552 | 475/18723 | 1.22e-03 | 5.97e-03 | 250 |
| GO:000930617 | Esophagus | ESCC | protein secretion | 190/8552 | 359/18723 | 3.22e-03 | 1.34e-02 | 190 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| MIA3 | SNV | Missense_Mutation | c.1863N>T | p.Glu621Asp | p.E621D | Q5JRA6 | protein_coding | tolerated(0.12) | benign(0.007) | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| MIA3 | SNV | Missense_Mutation | c.3776C>G | p.Ser1259Cys | p.S1259C | Q5JRA6 | protein_coding | deleterious(0.03) | probably_damaging(0.94) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| MIA3 | SNV | Missense_Mutation | novel | c.2476N>C | p.Glu826Gln | p.E826Q | Q5JRA6 | protein_coding | tolerated(0.13) | benign(0.131) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| MIA3 | SNV | Missense_Mutation | novel | c.3970N>A | p.Glu1324Lys | p.E1324K | Q5JRA6 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| MIA3 | SNV | Missense_Mutation | c.1836N>T | p.Glu612Asp | p.E612D | Q5JRA6 | protein_coding | tolerated(0.12) | possibly_damaging(0.681) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| MIA3 | SNV | Missense_Mutation | rs199732400 | c.1159A>G | p.Ile387Val | p.I387V | Q5JRA6 | protein_coding | tolerated(0.57) | benign(0) | TCGA-B6-A2IU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| MIA3 | SNV | Missense_Mutation | c.4900G>A | p.Ala1634Thr | p.A1634T | Q5JRA6 | protein_coding | tolerated(0.05) | possibly_damaging(0.802) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| MIA3 | SNV | Missense_Mutation | c.3496N>C | p.Asp1166His | p.D1166H | Q5JRA6 | protein_coding | deleterious(0) | possibly_damaging(0.907) | TCGA-BH-A18Q-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| MIA3 | SNV | Missense_Mutation | c.815N>G | p.Thr272Ser | p.T272S | Q5JRA6 | protein_coding | tolerated(0.38) | benign(0.031) | TCGA-BH-A1FU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| MIA3 | SNV | Missense_Mutation | c.1276G>A | p.Gly426Arg | p.G426R | Q5JRA6 | protein_coding | tolerated(0.48) | benign(0.009) | TCGA-C8-A131-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 |
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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 |
| Page: 1 |
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