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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:0007586 | Stomach | GC | digestion | 38/1159 | 137/18723 | 1.80e-15 | 1.22e-12 | 38 |
| GO:00987546 | Stomach | GC | detoxification | 37/1159 | 152/18723 | 3.63e-13 | 1.52e-10 | 37 |
| GO:00226006 | Stomach | GC | digestive system process | 30/1159 | 104/18723 | 5.40e-13 | 2.10e-10 | 30 |
| GO:00096366 | Stomach | GC | response to toxic substance | 50/1159 | 262/18723 | 7.42e-13 | 2.69e-10 | 50 |
| GO:00508925 | Stomach | GC | intestinal absorption | 18/1159 | 41/18723 | 8.10e-12 | 2.20e-09 | 18 |
| GO:00972376 | Stomach | GC | cellular response to toxic substance | 31/1159 | 124/18723 | 1.40e-11 | 3.31e-09 | 31 |
| GO:19907486 | Stomach | GC | cellular detoxification | 29/1159 | 116/18723 | 6.36e-11 | 1.19e-08 | 29 |
| GO:00988696 | Stomach | GC | cellular oxidant detoxification | 24/1159 | 101/18723 | 8.32e-09 | 8.22e-07 | 24 |
| GO:00066315 | Stomach | GC | fatty acid metabolic process | 55/1159 | 390/18723 | 8.63e-09 | 8.38e-07 | 55 |
| GO:00069796 | Stomach | GC | response to oxidative stress | 60/1159 | 446/18723 | 1.10e-08 | 1.01e-06 | 60 |
| GO:0006641 | Stomach | GC | triglyceride metabolic process | 23/1159 | 100/18723 | 3.27e-08 | 2.44e-06 | 23 |
| GO:0098856 | Stomach | GC | intestinal lipid absorption | 10/1159 | 21/18723 | 1.50e-07 | 8.56e-06 | 10 |
| GO:00725936 | Stomach | GC | reactive oxygen species metabolic process | 37/1159 | 239/18723 | 2.28e-07 | 1.23e-05 | 37 |
| GO:0006639 | Stomach | GC | acylglycerol metabolic process | 24/1159 | 128/18723 | 9.59e-07 | 4.53e-05 | 24 |
| GO:0006638 | Stomach | GC | neutral lipid metabolic process | 24/1159 | 129/18723 | 1.11e-06 | 5.20e-05 | 24 |
| GO:00621976 | Stomach | GC | cellular response to chemical stress | 44/1159 | 337/18723 | 2.24e-06 | 9.73e-05 | 44 |
| GO:00442424 | Stomach | GC | cellular lipid catabolic process | 32/1159 | 214/18723 | 3.16e-06 | 1.29e-04 | 32 |
| GO:00003026 | Stomach | GC | response to reactive oxygen species | 32/1159 | 222/18723 | 6.94e-06 | 2.57e-04 | 32 |
| GO:00160425 | Stomach | GC | lipid catabolic process | 41/1159 | 320/18723 | 7.84e-06 | 2.80e-04 | 41 |
| GO:00345996 | Stomach | GC | cellular response to oxidative stress | 38/1159 | 288/18723 | 8.45e-06 | 2.96e-04 | 38 |
| 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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