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Gene: APOBEC3A |
Gene summary for APOBEC3A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | APOBEC3A | Gene ID | 200315 |
| Gene name | apolipoprotein B mRNA editing enzyme catalytic subunit 3A | |
| Gene Alias | A3A | |
| Cytomap | 22q13.1 | |
| Gene Type | protein-coding | GO ID | GO:0002376 | UniProtAcc | B7ZLZ1 |
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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 |
| 200315 | APOBEC3A | P1T-E | Human | Esophagus | ESCC | 1.22e-06 | 2.42e+00 | 0.0875 |
| 200315 | APOBEC3A | P4T-E | Human | Esophagus | ESCC | 2.67e-11 | 8.14e-01 | 0.1323 |
| 200315 | APOBEC3A | P23T-E | Human | Esophagus | ESCC | 2.52e-07 | 1.24e+00 | 0.108 |
| 200315 | APOBEC3A | P80T-E | Human | Esophagus | ESCC | 5.04e-09 | 1.80e+00 | 0.155 |
| 200315 | APOBEC3A | P84T-E | Human | Esophagus | ESCC | 1.40e-03 | 1.32e+00 | 0.0933 |
| 200315 | APOBEC3A | P127T-E | Human | Esophagus | ESCC | 8.44e-10 | 1.09e+00 | 0.0826 |
| 200315 | APOBEC3A | HCC1 | Human | Liver | HCC | 1.89e-02 | 4.80e-01 | 0.5336 |
| 200315 | APOBEC3A | HCC2 | Human | Liver | HCC | 1.12e-12 | 5.86e-01 | 0.5341 |
| 200315 | APOBEC3A | HCC5 | Human | Liver | HCC | 2.42e-07 | 6.06e-01 | 0.4932 |
| 200315 | APOBEC3A | C04 | Human | Oral cavity | OSCC | 1.78e-09 | 1.69e+00 | 0.2633 |
| 200315 | APOBEC3A | C21 | Human | Oral cavity | OSCC | 1.09e-03 | 1.42e+00 | 0.2678 |
| 200315 | APOBEC3A | C46 | Human | Oral cavity | OSCC | 6.59e-08 | 1.05e+00 | 0.1673 |
| 200315 | APOBEC3A | C57 | Human | Oral cavity | OSCC | 2.15e-51 | 3.49e+00 | 0.1679 |
| 200315 | APOBEC3A | C08 | Human | Oral cavity | OSCC | 1.03e-05 | 1.93e+00 | 0.1919 |
| 200315 | APOBEC3A | C86 | Human | Oral cavity | OSCC | 1.64e-02 | 2.66e+00 | 0.161 |
| 200315 | APOBEC3A | LN22 | Human | Oral cavity | OSCC | 2.90e-02 | 2.62e-01 | 0.1733 |
| 200315 | APOBEC3A | LN46 | Human | Oral cavity | OSCC | 3.02e-11 | 1.66e+00 | 0.1666 |
| Page: 1 |
| 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:0016032111 | Esophagus | ESCC | viral process | 301/8552 | 415/18723 | 3.34e-29 | 1.32e-26 | 301 |
| GO:0019058111 | Esophagus | ESCC | viral life cycle | 226/8552 | 317/18723 | 1.17e-20 | 1.76e-18 | 226 |
| GO:0034655110 | Esophagus | ESCC | nucleobase-containing compound catabolic process | 272/8552 | 407/18723 | 2.92e-18 | 2.90e-16 | 272 |
| GO:004670018 | Esophagus | ESCC | heterocycle catabolic process | 286/8552 | 445/18723 | 1.12e-15 | 7.47e-14 | 286 |
| GO:004427019 | Esophagus | ESCC | cellular nitrogen compound catabolic process | 288/8552 | 451/18723 | 3.03e-15 | 1.79e-13 | 288 |
| GO:001943918 | Esophagus | ESCC | aromatic compound catabolic process | 295/8552 | 467/18723 | 1.09e-14 | 5.98e-13 | 295 |
| GO:0019079111 | Esophagus | ESCC | viral genome replication | 102/8552 | 131/18723 | 4.31e-14 | 2.19e-12 | 102 |
| GO:000961518 | Esophagus | ESCC | response to virus | 238/8552 | 367/18723 | 6.65e-14 | 3.32e-12 | 238 |
| GO:190136118 | Esophagus | ESCC | organic cyclic compound catabolic process | 307/8552 | 495/18723 | 9.99e-14 | 4.80e-12 | 307 |
| GO:0050792111 | Esophagus | ESCC | regulation of viral process | 119/8552 | 164/18723 | 2.19e-12 | 9.03e-11 | 119 |
| GO:1903900111 | Esophagus | ESCC | regulation of viral life cycle | 106/8552 | 148/18723 | 1.26e-10 | 3.72e-09 | 106 |
| GO:0045069110 | Esophagus | ESCC | regulation of viral genome replication | 67/8552 | 85/18723 | 3.81e-10 | 1.04e-08 | 67 |
| GO:00516075 | Esophagus | ESCC | defense response to virus | 171/8552 | 265/18723 | 3.91e-10 | 1.05e-08 | 171 |
| GO:01405465 | Esophagus | ESCC | defense response to symbiont | 171/8552 | 265/18723 | 3.91e-10 | 1.05e-08 | 171 |
| GO:00094512 | Esophagus | ESCC | RNA modification | 114/8552 | 167/18723 | 2.76e-09 | 6.04e-08 | 114 |
| GO:004852516 | Esophagus | ESCC | negative regulation of viral process | 66/8552 | 92/18723 | 3.49e-07 | 4.88e-06 | 66 |
| GO:004507114 | Esophagus | ESCC | negative regulation of viral genome replication | 44/8552 | 56/18723 | 4.84e-07 | 6.50e-06 | 44 |
| GO:000941020 | Esophagus | ESCC | response to xenobiotic stimulus | 253/8552 | 462/18723 | 4.55e-05 | 3.58e-04 | 253 |
| GO:003969411 | Esophagus | ESCC | viral RNA genome replication | 27/8552 | 35/18723 | 1.48e-04 | 9.88e-04 | 27 |
| GO:19016574 | Esophagus | ESCC | glycosyl compound metabolic process | 57/8552 | 88/18723 | 2.32e-04 | 1.44e-03 | 57 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05170210 | Esophagus | ESCC | Human immunodeficiency virus 1 infection | 147/4205 | 212/8465 | 3.37e-09 | 3.53e-08 | 1.81e-08 | 147 |
| hsa0517038 | Esophagus | ESCC | Human immunodeficiency virus 1 infection | 147/4205 | 212/8465 | 3.37e-09 | 3.53e-08 | 1.81e-08 | 147 |
| hsa032502 | Liver | HCC | Viral life cycle - HIV-1 | 46/4020 | 63/8465 | 3.25e-05 | 1.88e-04 | 1.04e-04 | 46 |
| hsa051709 | Liver | HCC | Human immunodeficiency virus 1 infection | 125/4020 | 212/8465 | 4.51e-04 | 1.94e-03 | 1.08e-03 | 125 |
| hsa0325011 | Liver | HCC | Viral life cycle - HIV-1 | 46/4020 | 63/8465 | 3.25e-05 | 1.88e-04 | 1.04e-04 | 46 |
| hsa0517012 | Liver | HCC | Human immunodeficiency virus 1 infection | 125/4020 | 212/8465 | 4.51e-04 | 1.94e-03 | 1.08e-03 | 125 |
| hsa0517027 | Oral cavity | OSCC | Human immunodeficiency virus 1 infection | 133/3704 | 212/8465 | 1.42e-08 | 1.40e-07 | 7.12e-08 | 133 |
| hsa032508 | Oral cavity | OSCC | Viral life cycle - HIV-1 | 45/3704 | 63/8465 | 7.62e-06 | 3.59e-05 | 1.83e-05 | 45 |
| hsa05170111 | Oral cavity | OSCC | Human immunodeficiency virus 1 infection | 133/3704 | 212/8465 | 1.42e-08 | 1.40e-07 | 7.12e-08 | 133 |
| hsa0325013 | Oral cavity | OSCC | Viral life cycle - HIV-1 | 45/3704 | 63/8465 | 7.62e-06 | 3.59e-05 | 1.83e-05 | 45 |
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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 |
| APOBEC3A | SNV | Missense_Mutation | novel | c.221N>A | p.Arg74His | p.R74H | P31941 | protein_coding | tolerated(0.16) | benign(0.238) | TCGA-A8-A083-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| APOBEC3A | SNV | Missense_Mutation | novel | c.221N>T | p.Arg74Leu | p.R74L | P31941 | protein_coding | tolerated(0.2) | benign(0.031) | TCGA-AC-A4ZE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| APOBEC3A | SNV | Missense_Mutation | c.554N>T | p.Ala185Val | p.A185V | P31941 | protein_coding | tolerated(0.29) | possibly_damaging(0.733) | TCGA-F4-6463-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| APOBEC3A | SNV | Missense_Mutation | novel | c.474N>G | p.Phe158Leu | p.F158L | P31941 | protein_coding | tolerated(0.2) | benign(0.37) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
| APOBEC3A | SNV | Missense_Mutation | novel | c.216N>T | p.Glu72Asp | p.E72D | P31941 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| APOBEC3A | SNV | Missense_Mutation | novel | c.242C>A | p.Ser81Tyr | p.S81Y | P31941 | protein_coding | tolerated(0.43) | benign(0.027) | TCGA-EO-A3B0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| APOBEC3A | SNV | Missense_Mutation | novel | c.288C>G | p.Ile96Met | p.I96M | P31941 | protein_coding | tolerated(0.11) | possibly_damaging(0.786) | TCGA-2Y-A9H1-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| APOBEC3A | SNV | Missense_Mutation | novel | c.257N>A | p.Pro86Gln | p.P86Q | P31941 | protein_coding | tolerated(0.43) | benign(0.11) | TCGA-05-4396-01 | Lung | lung adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| APOBEC3A | SNV | Missense_Mutation | novel | c.44C>A | p.Pro15Gln | p.P15Q | P31941 | protein_coding | tolerated(0.5) | benign(0.302) | TCGA-55-6987-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| APOBEC3A | SNV | Missense_Mutation | c.172C>A | p.Gln58Lys | p.Q58K | P31941 | protein_coding | tolerated(0.29) | benign(0.003) | TCGA-62-A46P-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
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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 |
| 200315 | APOBEC3A | ENZYME, DRUGGABLE GENOME | GNF-PF-3314 | CHEMBL582287 | ||
| 200315 | APOBEC3A | ENZYME, DRUGGABLE GENOME | GNF-PF-4665 | CHEMBL601744 | ||
| 200315 | APOBEC3A | ENZYME, DRUGGABLE GENOME | GNF-PF-4242 | CHEMBL584514 | ||
| 200315 | APOBEC3A | ENZYME, DRUGGABLE GENOME | CEFOTETAN | CEFOTETAN | ||
| 200315 | APOBEC3A | ENZYME, DRUGGABLE GENOME | MYRICETIN | MYRICETIN | ||
| 200315 | APOBEC3A | ENZYME, DRUGGABLE GENOME | GNF-PF-4464 | CHEMBL600692 | ||
| 200315 | APOBEC3A | ENZYME, DRUGGABLE GENOME | GNF-PF-3352 | CHEMBL600306 | ||
| 200315 | APOBEC3A | ENZYME, DRUGGABLE GENOME | DIMETHYLPHENYLPIPERAZINIUM IODIDE | DIMETHYLPHENYLPIPERAZINIUM IODIDE | ||
| 200315 | APOBEC3A | ENZYME, DRUGGABLE GENOME | TCMDC-124266 | CHEMBL124006 | ||
| 200315 | APOBEC3A | ENZYME, DRUGGABLE GENOME | NSC-50690 | CHEMBL1388703 |
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