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Gene: APOA4 |
Gene summary for APOA4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | APOA4 | Gene ID | 337 |
| Gene name | apolipoprotein A4 | |
| Gene Alias | APOA4 | |
| Cytomap | 11q23.3 | |
| Gene Type | protein-coding | GO ID | GO:0000302 | UniProtAcc | NA |
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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 |
| 337 | APOA4 | Pat01-B | Human | Stomach | GC | 1.35e-59 | 1.55e+00 | 0.5754 |
| 337 | APOA4 | Pat02-B | Human | Stomach | GC | 1.67e-02 | 2.55e-01 | 0.0368 |
| 337 | APOA4 | Pat03-B | Human | Stomach | GC | 1.79e-28 | 1.10e+00 | 0.3693 |
| 337 | APOA4 | Pat05-B | Human | Stomach | GC | 1.21e-02 | 3.68e-01 | -0.0353 |
| 337 | APOA4 | Pat17-B | Human | Stomach | GC | 6.74e-23 | 9.43e-01 | 0.3109 |
| 337 | APOA4 | SIM_1 | Human | Stomach | SIM | 9.31e-09 | 5.29e-01 | 0.3573 |
| 337 | APOA4 | SIM_4 | Human | Stomach | SIM | 5.47e-13 | 5.93e-01 | 0.2664 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:00465031 | Stomach | SIM | glycerolipid catabolic process | 9/708 | 65/18723 | 7.22e-04 | 1.04e-02 | 9 |
| GO:0034368 | Stomach | SIM | protein-lipid complex remodeling | 6/708 | 30/18723 | 7.81e-04 | 1.08e-02 | 6 |
| GO:0034369 | Stomach | SIM | plasma lipoprotein particle remodeling | 6/708 | 30/18723 | 7.81e-04 | 1.08e-02 | 6 |
| GO:0065005 | Stomach | SIM | protein-lipid complex assembly | 6/708 | 31/18723 | 9.38e-04 | 1.25e-02 | 6 |
| GO:00159141 | Stomach | SIM | phospholipid transport | 11/708 | 96/18723 | 9.94e-04 | 1.31e-02 | 11 |
| GO:0034367 | Stomach | SIM | protein-containing complex remodeling | 6/708 | 32/18723 | 1.12e-03 | 1.44e-02 | 6 |
| GO:0097006 | Stomach | SIM | regulation of plasma lipoprotein particle levels | 10/708 | 85/18723 | 1.36e-03 | 1.67e-02 | 10 |
| GO:0019430 | Stomach | SIM | removal of superoxide radicals | 5/708 | 23/18723 | 1.45e-03 | 1.75e-02 | 5 |
| GO:00108961 | Stomach | SIM | regulation of triglyceride catabolic process | 4/708 | 14/18723 | 1.50e-03 | 1.77e-02 | 4 |
| GO:0071827 | Stomach | SIM | plasma lipoprotein particle organization | 7/708 | 46/18723 | 1.59e-03 | 1.85e-02 | 7 |
| GO:00108764 | Stomach | SIM | lipid localization | 30/708 | 448/18723 | 1.87e-03 | 2.08e-02 | 30 |
| GO:0120009 | Stomach | SIM | intermembrane lipid transfer | 7/708 | 48/18723 | 2.05e-03 | 2.21e-02 | 7 |
| GO:000606611 | Stomach | SIM | alcohol metabolic process | 25/708 | 353/18723 | 2.07e-03 | 2.22e-02 | 25 |
| GO:0071450 | Stomach | SIM | cellular response to oxygen radical | 5/708 | 25/18723 | 2.16e-03 | 2.26e-02 | 5 |
| GO:0071451 | Stomach | SIM | cellular response to superoxide | 5/708 | 25/18723 | 2.16e-03 | 2.26e-02 | 5 |
| GO:00157481 | Stomach | SIM | organophosphate ester transport | 13/708 | 140/18723 | 2.54e-03 | 2.54e-02 | 13 |
| GO:00068693 | Stomach | SIM | lipid transport | 27/708 | 398/18723 | 2.58e-03 | 2.55e-02 | 27 |
| GO:0071825 | Stomach | SIM | protein-lipid complex subunit organization | 7/708 | 50/18723 | 2.60e-03 | 2.55e-02 | 7 |
| GO:0000303 | Stomach | SIM | response to superoxide | 5/708 | 28/18723 | 3.63e-03 | 3.37e-02 | 5 |
| GO:00302991 | Stomach | SIM | intestinal cholesterol absorption | 4/708 | 18/18723 | 4.06e-03 | 3.66e-02 | 4 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0541712 | Stomach | GC | Lipid and atherosclerosis | 40/708 | 215/8465 | 1.01e-06 | 1.80e-05 | 1.27e-05 | 40 |
| hsa04975 | Stomach | GC | Fat digestion and absorption | 14/708 | 43/8465 | 5.71e-06 | 8.30e-05 | 5.84e-05 | 14 |
| hsa0541713 | Stomach | GC | Lipid and atherosclerosis | 40/708 | 215/8465 | 1.01e-06 | 1.80e-05 | 1.27e-05 | 40 |
| hsa049751 | Stomach | GC | Fat digestion and absorption | 14/708 | 43/8465 | 5.71e-06 | 8.30e-05 | 5.84e-05 | 14 |
| hsa0541710 | Stomach | SIM | Lipid and atherosclerosis | 34/465 | 215/8465 | 1.80e-08 | 4.20e-07 | 3.37e-07 | 34 |
| hsa049752 | Stomach | SIM | Fat digestion and absorption | 12/465 | 43/8465 | 2.11e-06 | 3.05e-05 | 2.45e-05 | 12 |
| hsa04979 | Stomach | SIM | Cholesterol metabolism | 8/465 | 51/8465 | 6.17e-03 | 3.83e-02 | 3.08e-02 | 8 |
| hsa0541711 | Stomach | SIM | Lipid and atherosclerosis | 34/465 | 215/8465 | 1.80e-08 | 4.20e-07 | 3.37e-07 | 34 |
| hsa049753 | Stomach | SIM | Fat digestion and absorption | 12/465 | 43/8465 | 2.11e-06 | 3.05e-05 | 2.45e-05 | 12 |
| hsa049791 | Stomach | SIM | Cholesterol metabolism | 8/465 | 51/8465 | 6.17e-03 | 3.83e-02 | 3.08e-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 |
| APOA4 | SNV | Missense_Mutation | novel | c.540G>C | p.Arg180Ser | p.R180S | P06727 | protein_coding | tolerated(0.48) | benign(0.007) | TCGA-A2-A0CU-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| APOA4 | SNV | Missense_Mutation | rs753407230 | c.428N>A | p.Arg143His | p.R143H | P06727 | protein_coding | tolerated(0.25) | benign(0.018) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| APOA4 | SNV | Missense_Mutation | c.685G>T | p.Asp229Tyr | p.D229Y | P06727 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | ||
| APOA4 | SNV | Missense_Mutation | rs771829056 | c.319N>A | p.Glu107Lys | p.E107K | P06727 | protein_coding | tolerated(0.09) | benign(0.049) | TCGA-GM-A2D9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| APOA4 | insertion | Frame_Shift_Ins | novel | c.538_539insTCTTCAGT | p.Arg180IlefsTer65 | p.R180Ifs*65 | P06727 | protein_coding | TCGA-A2-A0CU-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| APOA4 | insertion | Frame_Shift_Ins | novel | c.968_969insGGCGAGCAGAACAGGGTCCCTGGCCCTGGGGGGCTCACAGT | p.Gln324AlafsTer31 | p.Q324Afs*31 | P06727 | protein_coding | TCGA-AN-A04A-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | ||
| APOA4 | SNV | Missense_Mutation | rs541515376 | c.659G>A | p.Arg220His | p.R220H | P06727 | protein_coding | deleterious(0.03) | possibly_damaging(0.54) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| APOA4 | SNV | Missense_Mutation | rs142295954 | c.505N>T | p.Arg169Trp | p.R169W | P06727 | protein_coding | deleterious(0.01) | benign(0.302) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
| APOA4 | SNV | Missense_Mutation | rs147626624 | c.605N>T | p.Thr202Met | p.T202M | P06727 | protein_coding | tolerated(0.13) | benign(0.241) | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| APOA4 | SNV | Missense_Mutation | c.1042N>G | p.Arg348Gly | p.R348G | P06727 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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