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Gene: CYP2D6 |
Gene summary for CYP2D6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CYP2D6 | Gene ID | 1565 |
| Gene name | cytochrome P450 family 2 subfamily D member 6 | |
| Gene Alias | CPD6 | |
| Cytomap | 22q13.2 | |
| Gene Type | protein-coding | GO ID | GO:0001523 | UniProtAcc | C1ID52 |
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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 |
| 1565 | CYP2D6 | Pat01-B | Human | Stomach | GC | 1.41e-02 | 1.09e-01 | 0.5754 |
| 1565 | CYP2D6 | Pat03-B | Human | Stomach | GC | 5.99e-11 | 2.79e-01 | 0.3693 |
| 1565 | CYP2D6 | Pat17-B | Human | Stomach | GC | 1.87e-04 | 1.65e-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 |
| ∗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:00066315 | Stomach | GC | fatty acid metabolic process | 55/1159 | 390/18723 | 8.63e-09 | 8.38e-07 | 55 |
| GO:00094106 | Stomach | GC | response to xenobiotic stimulus | 61/1159 | 462/18723 | 1.68e-08 | 1.43e-06 | 61 |
| GO:0033559 | Stomach | GC | unsaturated fatty acid metabolic process | 24/1159 | 116/18723 | 1.43e-07 | 8.35e-06 | 24 |
| GO:0006690 | Stomach | GC | icosanoid metabolic process | 24/1159 | 123/18723 | 4.49e-07 | 2.32e-05 | 24 |
| GO:00510986 | Stomach | GC | regulation of binding | 46/1159 | 363/18723 | 3.02e-06 | 1.25e-04 | 46 |
| GO:0120254 | Stomach | GC | olefinic compound metabolic process | 25/1159 | 153/18723 | 7.68e-06 | 2.77e-04 | 25 |
| GO:00343084 | Stomach | GC | primary alcohol metabolic process | 19/1159 | 102/18723 | 1.40e-05 | 4.54e-04 | 19 |
| GO:0006633 | Stomach | GC | fatty acid biosynthetic process | 25/1159 | 163/18723 | 2.36e-05 | 6.90e-04 | 25 |
| GO:0006805 | Stomach | GC | xenobiotic metabolic process | 19/1159 | 111/18723 | 4.79e-05 | 1.15e-03 | 19 |
| GO:00060665 | Stomach | GC | alcohol metabolic process | 41/1159 | 353/18723 | 7.85e-05 | 1.68e-03 | 41 |
| GO:0042445 | Stomach | GC | hormone metabolic process | 29/1159 | 218/18723 | 8.22e-05 | 1.75e-03 | 29 |
| GO:00463944 | Stomach | GC | carboxylic acid biosynthetic process | 37/1159 | 314/18723 | 1.28e-04 | 2.41e-03 | 37 |
| GO:00160534 | Stomach | GC | organic acid biosynthetic process | 37/1159 | 316/18723 | 1.46e-04 | 2.67e-03 | 37 |
| GO:0042572 | Stomach | GC | retinol metabolic process | 11/1159 | 50/18723 | 1.95e-04 | 3.33e-03 | 11 |
| GO:0072330 | Stomach | GC | monocarboxylic acid biosynthetic process | 27/1159 | 214/18723 | 3.41e-04 | 5.40e-03 | 27 |
| GO:0071466 | Stomach | GC | cellular response to xenobiotic stimulus | 23/1159 | 177/18723 | 6.01e-04 | 8.17e-03 | 23 |
| GO:0034754 | Stomach | GC | cellular hormone metabolic process | 19/1159 | 137/18723 | 7.88e-04 | 1.01e-02 | 19 |
| GO:0019369 | Stomach | GC | arachidonic acid metabolic process | 11/1159 | 59/18723 | 8.75e-04 | 1.09e-02 | 11 |
| GO:0006721 | Stomach | GC | terpenoid metabolic process | 15/1159 | 97/18723 | 8.84e-04 | 1.09e-02 | 15 |
| GO:00511005 | Stomach | GC | negative regulation of binding | 21/1159 | 162/18723 | 1.05e-03 | 1.24e-02 | 21 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| CYP2D6 | SNV | Missense_Mutation | c.859N>A | p.Glu287Lys | p.E287K | P10635 | protein_coding | tolerated(0.13) | benign(0.044) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CYP2D6 | SNV | Missense_Mutation | novel | c.175G>A | p.Asp59Asn | p.D59N | P10635 | protein_coding | tolerated(0.57) | benign(0.001) | TCGA-BH-AB28-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | SD |
| CYP2D6 | SNV | Missense_Mutation | novel | c.1052N>A | p.Ala351Asp | p.A351D | P10635 | protein_coding | tolerated(0.29) | possibly_damaging(0.768) | TCGA-E9-A3X8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphane | CR |
| CYP2D6 | SNV | Missense_Mutation | novel | c.769N>A | p.Glu257Lys | p.E257K | P10635 | protein_coding | tolerated(0.27) | possibly_damaging(0.868) | TCGA-GM-A3XL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | CR |
| CYP2D6 | insertion | Frame_Shift_Ins | novel | c.395_396insA | p.Arg133AlafsTer121 | p.R133Afs*121 | P10635 | protein_coding | TCGA-AO-A0J6-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| CYP2D6 | SNV | Missense_Mutation | novel | c.187N>T | p.Arg63Cys | p.R63C | P10635 | protein_coding | tolerated(0.13) | benign(0.026) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CYP2D6 | SNV | Missense_Mutation | rs556882139 | c.518G>A | p.Arg173His | p.R173H | P10635 | protein_coding | deleterious(0.03) | benign(0.006) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| CYP2D6 | SNV | Missense_Mutation | c.509G>A | p.Arg170His | p.R170H | P10635 | protein_coding | tolerated(0.32) | benign(0.009) | TCGA-AA-3655-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| CYP2D6 | SNV | Missense_Mutation | rs774382844 | c.1045N>A | p.Asp349Asn | p.D349N | P10635 | protein_coding | deleterious(0.01) | possibly_damaging(0.816) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| CYP2D6 | SNV | Missense_Mutation | rs769351604 | c.1093N>T | p.Arg365Cys | p.R365C | P10635 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AA-A00N-01 | Colorectum | colon 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 |
| 1565 | CYP2D6 | CYTOCHROME P450, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | FLUNISOLIDE | FLUNISOLIDE | 22931300 | |
| 1565 | CYP2D6 | CYTOCHROME P450, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | L-701324 | CHEMBL31741 | ||
| 1565 | CYP2D6 | CYTOCHROME P450, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | RANITIDINE | RANITIDINE | 22931300 | |
| 1565 | CYP2D6 | CYTOCHROME P450, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | NS-398 | NS-398 | ||
| 1565 | CYP2D6 | CYTOCHROME P450, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | Trimipramine | TRIMIPRAMINE | ||
| 1565 | CYP2D6 | CYTOCHROME P450, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | TICRYNAFEN | TICRYNAFEN | 22931300 | |
| 1565 | CYP2D6 | CYTOCHROME P450, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | PARAROSANILINE | PARAROSANILINE | ||
| 1565 | CYP2D6 | CYTOCHROME P450, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | ethanol | ALCOHOL | 24611668 | |
| 1565 | CYP2D6 | CYTOCHROME P450, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | ketorolac | KETOROLAC | 17986163 | |
| 1565 | CYP2D6 | CYTOCHROME P450, DRUGGABLE GENOME, CLINICALLY ACTIONABLE, ENZYME | CLEBOPRIDE | CLEBOPRIDE |
| 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 |
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