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Gene: ATOX1 |
Gene summary for ATOX1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ATOX1 | Gene ID | 475 |
| Gene name | antioxidant 1 copper chaperone | |
| Gene Alias | ATX1 | |
| Cytomap | 5q33.1 | |
| Gene Type | protein-coding | GO ID | GO:0000041 | UniProtAcc | O00244 |
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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 |
| 475 | ATOX1 | GSM4909281 | Human | Breast | IDC | 4.53e-10 | 4.22e-01 | 0.21 |
| 475 | ATOX1 | GSM4909285 | Human | Breast | IDC | 8.16e-04 | 2.68e-01 | 0.21 |
| 475 | ATOX1 | GSM4909286 | Human | Breast | IDC | 1.68e-09 | -3.73e-01 | 0.1081 |
| 475 | ATOX1 | GSM4909289 | Human | Breast | IDC | 2.86e-02 | 4.63e-01 | 0.1064 |
| 475 | ATOX1 | GSM4909291 | Human | Breast | IDC | 1.71e-18 | 6.06e-01 | 0.1753 |
| 475 | ATOX1 | GSM4909293 | Human | Breast | IDC | 2.38e-28 | 6.18e-01 | 0.1581 |
| 475 | ATOX1 | GSM4909294 | Human | Breast | IDC | 1.30e-37 | 6.99e-01 | 0.2022 |
| 475 | ATOX1 | GSM4909296 | Human | Breast | IDC | 1.14e-16 | 3.98e-01 | 0.1524 |
| 475 | ATOX1 | GSM4909297 | Human | Breast | IDC | 3.86e-14 | -6.55e-03 | 0.1517 |
| 475 | ATOX1 | GSM4909298 | Human | Breast | IDC | 6.97e-33 | 6.54e-01 | 0.1551 |
| 475 | ATOX1 | GSM4909299 | Human | Breast | IDC | 2.55e-04 | 3.26e-01 | 0.035 |
| 475 | ATOX1 | GSM4909301 | Human | Breast | IDC | 2.56e-25 | 5.81e-01 | 0.1577 |
| 475 | ATOX1 | GSM4909306 | Human | Breast | IDC | 1.03e-18 | 5.47e-01 | 0.1564 |
| 475 | ATOX1 | GSM4909307 | Human | Breast | IDC | 2.52e-08 | 3.81e-01 | 0.1569 |
| 475 | ATOX1 | GSM4909308 | Human | Breast | IDC | 3.49e-02 | 1.80e-01 | 0.158 |
| 475 | ATOX1 | GSM4909311 | Human | Breast | IDC | 3.35e-35 | 1.45e-01 | 0.1534 |
| 475 | ATOX1 | GSM4909312 | Human | Breast | IDC | 4.75e-11 | 1.62e-01 | 0.1552 |
| 475 | ATOX1 | GSM4909313 | Human | Breast | IDC | 1.41e-09 | 3.58e-01 | 0.0391 |
| 475 | ATOX1 | GSM4909315 | Human | Breast | IDC | 1.14e-37 | 7.73e-01 | 0.21 |
| 475 | ATOX1 | GSM4909316 | Human | Breast | IDC | 2.46e-32 | 8.97e-01 | 0.21 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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 |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:00000412 | Breast | Precancer | transition metal ion transport | 13/1080 | 105/18723 | 7.35e-03 | 4.89e-02 | 13 |
| GO:0070839 | Breast | IDC | metal ion export | 10/1434 | 54/18723 | 7.22e-03 | 4.96e-02 | 10 |
| GO:00708391 | Breast | DCIS | metal ion export | 10/1390 | 54/18723 | 5.83e-03 | 4.18e-02 | 10 |
| GO:00000411 | Liver | HCC | transition metal ion transport | 59/7958 | 105/18723 | 3.18e-03 | 1.47e-02 | 59 |
| GO:0006825 | Prostate | BPH | copper ion transport | 7/3107 | 15/18723 | 6.42e-03 | 2.91e-02 | 7 |
| GO:00068251 | Prostate | Tumor | copper ion transport | 7/3246 | 15/18723 | 8.22e-03 | 3.60e-02 | 7 |
| GO:0000041 | Stomach | GC | transition metal ion transport | 15/1159 | 105/18723 | 2.01e-03 | 2.03e-02 | 15 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0497821 | Breast | DCIS | Mineral absorption | 13/846 | 60/8465 | 5.48e-03 | 2.81e-02 | 2.07e-02 | 13 |
| hsa0497831 | Breast | DCIS | Mineral absorption | 13/846 | 60/8465 | 5.48e-03 | 2.81e-02 | 2.07e-02 | 13 |
| hsa0497814 | Prostate | BPH | Mineral absorption | 20/1718 | 60/8465 | 1.22e-02 | 3.61e-02 | 2.23e-02 | 20 |
| hsa0497815 | Prostate | BPH | Mineral absorption | 20/1718 | 60/8465 | 1.22e-02 | 3.61e-02 | 2.23e-02 | 20 |
| hsa049786 | Stomach | CAG | Mineral absorption | 8/368 | 60/8465 | 4.18e-03 | 2.94e-02 | 2.36e-02 | 8 |
| hsa049787 | Stomach | CAG | Mineral absorption | 8/368 | 60/8465 | 4.18e-03 | 2.94e-02 | 2.36e-02 | 8 |
| 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 |
| ATOX1 | SNV | Missense_Mutation | novel | c.52N>A | p.Ala18Thr | p.A18T | O00244 | protein_coding | tolerated(0.06) | probably_damaging(0.999) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ATOX1 | SNV | Missense_Mutation | novel | c.18C>A | p.Phe6Leu | p.F6L | O00244 | protein_coding | deleterious(0.02) | probably_damaging(0.992) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ATOX1 | insertion | Frame_Shift_Ins | novel | c.111_112insCACTCCA | p.Lys38HisfsTer8 | p.K38Hfs*8 | O00244 | protein_coding | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD | ||
| ATOX1 | SNV | Missense_Mutation | rs752342635 | c.5N>T | p.Pro2Leu | p.P2L | O00244 | protein_coding | tolerated(0.24) | benign(0) | TCGA-G3-AAV4-01 | Liver | liver hepatocellular carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 |
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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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