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Gene: CYP3A4 |
Gene summary for CYP3A4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CYP3A4 | Gene ID | 1576 |
| Gene name | cytochrome P450 family 3 subfamily A member 4 | |
| Gene Alias | CP33 | |
| Cytomap | 7q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0001523 | UniProtAcc | P08684 |
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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 |
| 1576 | CYP3A4 | S41 | Human | Liver | Cirrhotic | 5.54e-05 | 8.42e-01 | -0.0343 |
| 1576 | CYP3A4 | S44 | Human | Liver | HCC | 4.13e-14 | 1.46e+00 | -0.0083 |
| 1576 | CYP3A4 | HCC1_Meng | Human | Liver | HCC | 4.93e-06 | -2.74e-01 | 0.0246 |
| 1576 | CYP3A4 | HCC2_Meng | Human | Liver | HCC | 2.30e-06 | -2.73e-01 | 0.0107 |
| 1576 | CYP3A4 | cirrhotic1 | Human | Liver | Cirrhotic | 3.31e-02 | -2.57e-01 | 0.0202 |
| 1576 | CYP3A4 | cirrhotic2 | Human | Liver | Cirrhotic | 8.39e-03 | -2.56e-01 | 0.0201 |
| 1576 | CYP3A4 | HCC2 | Human | Liver | HCC | 2.27e-03 | 1.99e+00 | 0.5341 |
| 1576 | CYP3A4 | Pt13.a | Human | Liver | HCC | 2.30e-06 | -2.74e-01 | 0.021 |
| 1576 | CYP3A4 | Pt14.d | Human | Liver | HCC | 2.60e-04 | -2.71e-01 | 0.0143 |
| 1576 | CYP3A4 | S027 | Human | Liver | HCC | 1.63e-02 | -8.16e-02 | 0.2446 |
| 1576 | CYP3A4 | Pat01-B | Human | Stomach | GC | 5.13e-24 | 5.68e-01 | 0.5754 |
| 1576 | CYP3A4 | Pat03-B | Human | Stomach | GC | 3.52e-08 | 2.74e-01 | 0.3693 |
| 1576 | CYP3A4 | Pat17-B | Human | Stomach | GC | 1.95e-05 | 2.45e-01 | 0.3109 |
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| 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 | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:190136111 | Liver | Cirrhotic | organic cyclic compound catabolic process | 213/4634 | 495/18723 | 1.58e-19 | 3.67e-17 | 213 |
| GO:004427011 | Liver | Cirrhotic | cellular nitrogen compound catabolic process | 195/4634 | 451/18723 | 2.99e-18 | 4.94e-16 | 195 |
| GO:000820211 | Liver | Cirrhotic | steroid metabolic process | 143/4634 | 319/18723 | 2.79e-15 | 3.18e-13 | 143 |
| GO:000663112 | Liver | Cirrhotic | fatty acid metabolic process | 165/4634 | 390/18723 | 1.29e-14 | 1.26e-12 | 165 |
| GO:001605312 | Liver | Cirrhotic | organic acid biosynthetic process | 139/4634 | 316/18723 | 4.28e-14 | 3.83e-12 | 139 |
| GO:004639412 | Liver | Cirrhotic | carboxylic acid biosynthetic process | 137/4634 | 314/18723 | 1.40e-13 | 1.14e-11 | 137 |
| GO:19026521 | Liver | Cirrhotic | secondary alcohol metabolic process | 75/4634 | 147/18723 | 5.62e-12 | 3.91e-10 | 75 |
| GO:004428211 | Liver | Cirrhotic | small molecule catabolic process | 151/4634 | 376/18723 | 2.20e-11 | 1.34e-09 | 151 |
| GO:00082031 | Liver | Cirrhotic | cholesterol metabolic process | 70/4634 | 137/18723 | 2.59e-11 | 1.55e-09 | 70 |
| GO:00161251 | Liver | Cirrhotic | sterol metabolic process | 75/4634 | 152/18723 | 4.54e-11 | 2.61e-09 | 75 |
| GO:000606612 | Liver | Cirrhotic | alcohol metabolic process | 141/4634 | 353/18723 | 1.57e-10 | 8.03e-09 | 141 |
| GO:007233011 | Liver | Cirrhotic | monocarboxylic acid biosynthetic process | 93/4634 | 214/18723 | 1.43e-09 | 6.16e-08 | 93 |
| GO:00066941 | Liver | Cirrhotic | steroid biosynthetic process | 77/4634 | 173/18723 | 1.02e-08 | 3.91e-07 | 77 |
| GO:000941012 | Liver | Cirrhotic | response to xenobiotic stimulus | 165/4634 | 462/18723 | 6.82e-08 | 2.09e-06 | 165 |
| GO:000663311 | Liver | Cirrhotic | fatty acid biosynthetic process | 70/4634 | 163/18723 | 2.57e-07 | 6.41e-06 | 70 |
| GO:001604212 | Liver | Cirrhotic | lipid catabolic process | 112/4634 | 320/18723 | 2.31e-05 | 3.03e-04 | 112 |
| GO:0046165 | Liver | Cirrhotic | alcohol biosynthetic process | 55/4634 | 140/18723 | 9.74e-05 | 1.03e-03 | 55 |
| GO:00714661 | Liver | Cirrhotic | cellular response to xenobiotic stimulus | 66/4634 | 177/18723 | 1.34e-04 | 1.31e-03 | 66 |
| GO:00067202 | Liver | Cirrhotic | isoprenoid metabolic process | 46/4634 | 116/18723 | 2.71e-04 | 2.41e-03 | 46 |
| GO:003025811 | Liver | Cirrhotic | lipid modification | 75/4634 | 212/18723 | 3.33e-04 | 2.87e-03 | 75 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa00983 | Liver | Cirrhotic | Drug metabolism - other enzymes | 34/2530 | 80/8465 | 1.08e-02 | 3.57e-02 | 2.20e-02 | 34 |
| hsa009831 | Liver | Cirrhotic | Drug metabolism - other enzymes | 34/2530 | 80/8465 | 1.08e-02 | 3.57e-02 | 2.20e-02 | 34 |
| hsa009832 | Liver | HCC | Drug metabolism - other enzymes | 54/4020 | 80/8465 | 2.25e-04 | 1.09e-03 | 6.08e-04 | 54 |
| hsa009833 | Liver | HCC | Drug metabolism - other enzymes | 54/4020 | 80/8465 | 2.25e-04 | 1.09e-03 | 6.08e-04 | 54 |
| hsa00980 | Stomach | GC | Metabolism of xenobiotics by cytochrome P450 | 15/708 | 78/8465 | 1.77e-03 | 1.16e-02 | 8.15e-03 | 15 |
| hsa009801 | Stomach | GC | Metabolism of xenobiotics by cytochrome P450 | 15/708 | 78/8465 | 1.77e-03 | 1.16e-02 | 8.15e-03 | 15 |
| 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 |
| CYP3A4 | SNV | Missense_Mutation | c.611N>G | p.Val204Gly | p.V204G | P08684 | protein_coding | deleterious(0.01) | probably_damaging(0.988) | TCGA-B6-A0X1-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| CYP3A4 | SNV | Missense_Mutation | c.624N>C | p.Lys208Asn | p.K208N | P08684 | protein_coding | deleterious(0.02) | benign(0.109) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CYP3A4 | insertion | Frame_Shift_Ins | novel | c.1493_1494insAGACAGAAAACATGTTTCCCTACACCTCTTGCATTCCATCCTCA | p.Thr499AspfsTer17 | p.T499Dfs*17 | P08684 | protein_coding | TCGA-A2-A0EV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| CYP3A4 | insertion | Frame_Shift_Ins | novel | c.1494_1495insCAATGCCTTCAAGCATTCCTTGTATTATG | p.Thr499GlnfsTer10 | p.T499Qfs*10 | P08684 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| CYP3A4 | SNV | Missense_Mutation | novel | c.544N>T | p.Asp182Tyr | p.D182Y | P08684 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| CYP3A4 | SNV | Missense_Mutation | c.216N>T | p.Trp72Cys | p.W72C | P08684 | protein_coding | deleterious(0) | possibly_damaging(0.664) | TCGA-A6-3809-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CYP3A4 | SNV | Missense_Mutation | rs199908125 | c.784G>A | p.Glu262Lys | p.E262K | P08684 | protein_coding | tolerated(1) | benign(0) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| CYP3A4 | SNV | Missense_Mutation | c.383G>T | p.Arg128Ile | p.R128I | P08684 | protein_coding | deleterious(0) | possibly_damaging(0.825) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| CYP3A4 | SNV | Missense_Mutation | c.1109N>T | p.Ala370Val | p.A370V | P08684 | protein_coding | tolerated(0.17) | benign(0.018) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| CYP3A4 | SNV | Missense_Mutation | novel | c.1170A>C | p.Lys390Asn | p.K390N | P08684 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| Page: 1 2 3 4 5 |
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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 |
| 1576 | CYP3A4 | ENZYME, DRUGGABLE GENOME, CYTOCHROME P450 | oxazepam | OXAZEPAM | ||
| 1576 | CYP3A4 | ENZYME, DRUGGABLE GENOME, CYTOCHROME P450 | FLUOXETINE HYDROCHLORIDE | FLUOXETINE HYDROCHLORIDE | ||
| 1576 | CYP3A4 | ENZYME, DRUGGABLE GENOME, CYTOCHROME P450 | ZM-336372 | CHEMBL186526 | ||
| 1576 | CYP3A4 | ENZYME, DRUGGABLE GENOME, CYTOCHROME P450 | DISULFIRAM | DISULFIRAM | ||
| 1576 | CYP3A4 | ENZYME, DRUGGABLE GENOME, CYTOCHROME P450 | SB-202190 | SB-202190 | ||
| 1576 | CYP3A4 | ENZYME, DRUGGABLE GENOME, CYTOCHROME P450 | IPRATROPIUM | IPRATROPIUM | 22931300 | |
| 1576 | CYP3A4 | ENZYME, DRUGGABLE GENOME, CYTOCHROME P450 | 2-(2-AMINOETHYL)ISOTHIOUREA DIHYDROBROMIDE | CHEMBL1256182 | ||
| 1576 | CYP3A4 | ENZYME, DRUGGABLE GENOME, CYTOCHROME P450 | BUTORPHANOL | BUTORPHANOL | 22931300 | |
| 1576 | CYP3A4 | ENZYME, DRUGGABLE GENOME, CYTOCHROME P450 | MRS-1523 | CHEMBL111545 | ||
| 1576 | CYP3A4 | ENZYME, DRUGGABLE GENOME, CYTOCHROME P450 | 5,7-DIMETHOXYISOFLAVONE | 5,7-DIMETHOXYISOFLAVONE |
| 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 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 |
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