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Gene: CYP2C9 |
Gene summary for CYP2C9 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CYP2C9 | Gene ID | 1559 |
| Gene name | cytochrome P450 family 2 subfamily C member 9 | |
| Gene Alias | CPC9 | |
| Cytomap | 10q23.33 | |
| Gene Type | protein-coding | GO ID | GO:0001676 | UniProtAcc | P11712 |
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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 |
| 1559 | CYP2C9 | NAFLD1 | Human | Liver | NAFLD | 8.12e-14 | 1.46e+00 | -0.04 |
| 1559 | CYP2C9 | S41 | Human | Liver | Cirrhotic | 2.55e-03 | 7.49e-01 | -0.0343 |
| 1559 | CYP2C9 | HCC1_Meng | Human | Liver | HCC | 6.63e-38 | -5.35e-01 | 0.0246 |
| 1559 | CYP2C9 | HCC2_Meng | Human | Liver | HCC | 7.46e-33 | -4.66e-01 | 0.0107 |
| 1559 | CYP2C9 | cirrhotic1 | Human | Liver | Cirrhotic | 5.01e-17 | -5.39e-01 | 0.0202 |
| 1559 | CYP2C9 | cirrhotic2 | Human | Liver | Cirrhotic | 5.10e-17 | -5.30e-01 | 0.0201 |
| 1559 | CYP2C9 | cirrhotic3 | Human | Liver | Cirrhotic | 2.24e-10 | -5.55e-01 | 0.0215 |
| 1559 | CYP2C9 | HCC1 | Human | Liver | HCC | 1.90e-08 | -4.59e-01 | 0.5336 |
| 1559 | CYP2C9 | HCC5 | Human | Liver | HCC | 2.83e-14 | -4.82e-01 | 0.4932 |
| 1559 | CYP2C9 | Pt13.a | Human | Liver | HCC | 6.57e-34 | -2.50e-01 | 0.021 |
| 1559 | CYP2C9 | Pt13.b | Human | Liver | HCC | 9.49e-47 | -2.87e-01 | 0.0251 |
| 1559 | CYP2C9 | Pt14.b | Human | Liver | HCC | 2.54e-16 | 3.97e-02 | 0.018 |
| 1559 | CYP2C9 | Pt14.d | Human | Liver | HCC | 4.46e-29 | -2.85e-01 | 0.0143 |
| 1559 | CYP2C9 | S015 | Human | Liver | HCC | 6.47e-09 | -5.24e-01 | 0.2375 |
| 1559 | CYP2C9 | S016 | Human | Liver | HCC | 3.89e-08 | -5.53e-01 | 0.2243 |
| 1559 | CYP2C9 | S027 | Human | Liver | HCC | 1.20e-02 | 5.35e-01 | 0.2446 |
| 1559 | CYP2C9 | S028 | Human | Liver | HCC | 5.54e-17 | 5.39e-01 | 0.2503 |
| 1559 | CYP2C9 | S029 | Human | Liver | HCC | 8.62e-07 | 4.40e-01 | 0.2581 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:00066316 | Liver | NAFLD | fatty acid metabolic process | 92/1882 | 390/18723 | 3.38e-15 | 3.29e-12 | 92 |
| GO:00160535 | Liver | NAFLD | organic acid biosynthetic process | 77/1882 | 316/18723 | 1.03e-13 | 6.69e-11 | 77 |
| GO:00463945 | Liver | NAFLD | carboxylic acid biosynthetic process | 75/1882 | 314/18723 | 6.37e-13 | 3.39e-10 | 75 |
| GO:00082023 | Liver | NAFLD | steroid metabolic process | 69/1882 | 319/18723 | 5.90e-10 | 1.28e-07 | 69 |
| GO:00094107 | Liver | NAFLD | response to xenobiotic stimulus | 88/1882 | 462/18723 | 2.53e-09 | 4.11e-07 | 88 |
| GO:00723303 | Liver | NAFLD | monocarboxylic acid biosynthetic process | 46/1882 | 214/18723 | 5.06e-07 | 3.07e-05 | 46 |
| GO:0008203 | Liver | NAFLD | cholesterol metabolic process | 32/1882 | 137/18723 | 4.28e-06 | 1.66e-04 | 32 |
| GO:0016125 | Liver | NAFLD | sterol metabolic process | 34/1882 | 152/18723 | 6.02e-06 | 2.11e-04 | 34 |
| GO:1902652 | Liver | NAFLD | secondary alcohol metabolic process | 33/1882 | 147/18723 | 7.57e-06 | 2.56e-04 | 33 |
| GO:00060666 | Liver | NAFLD | alcohol metabolic process | 62/1882 | 353/18723 | 9.01e-06 | 2.96e-04 | 62 |
| GO:0019627 | Liver | NAFLD | urea metabolic process | 7/1882 | 12/18723 | 5.15e-05 | 1.19e-03 | 7 |
| GO:0071941 | Liver | NAFLD | nitrogen cycle metabolic process | 7/1882 | 12/18723 | 5.15e-05 | 1.19e-03 | 7 |
| GO:00714663 | Liver | NAFLD | cellular response to xenobiotic stimulus | 33/1882 | 177/18723 | 3.54e-04 | 5.36e-03 | 33 |
| GO:00335596 | Liver | NAFLD | unsaturated fatty acid metabolic process | 24/1882 | 116/18723 | 4.64e-04 | 6.74e-03 | 24 |
| GO:00016763 | Liver | NAFLD | long-chain fatty acid metabolic process | 23/1882 | 112/18723 | 6.73e-04 | 8.66e-03 | 23 |
| GO:01202545 | Liver | NAFLD | olefinic compound metabolic process | 28/1882 | 153/18723 | 1.28e-03 | 1.45e-02 | 28 |
| GO:00068054 | Liver | NAFLD | xenobiotic metabolic process | 22/1882 | 111/18723 | 1.42e-03 | 1.58e-02 | 22 |
| GO:00066334 | Liver | NAFLD | fatty acid biosynthetic process | 29/1882 | 163/18723 | 1.67e-03 | 1.74e-02 | 29 |
| GO:00424452 | Liver | NAFLD | hormone metabolic process | 36/1882 | 218/18723 | 1.98e-03 | 1.98e-02 | 36 |
| GO:0070988 | Liver | NAFLD | demethylation | 16/1882 | 73/18723 | 2.09e-03 | 2.06e-02 | 16 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0541714 | Liver | NAFLD | Lipid and atherosclerosis | 42/1043 | 215/8465 | 1.46e-03 | 1.71e-02 | 1.38e-02 | 42 |
| hsa0541715 | Liver | NAFLD | Lipid and atherosclerosis | 42/1043 | 215/8465 | 1.46e-03 | 1.71e-02 | 1.38e-02 | 42 |
| hsa0541722 | Liver | Cirrhotic | Lipid and atherosclerosis | 80/2530 | 215/8465 | 1.18e-02 | 3.81e-02 | 2.35e-02 | 80 |
| hsa0541732 | Liver | Cirrhotic | Lipid and atherosclerosis | 80/2530 | 215/8465 | 1.18e-02 | 3.81e-02 | 2.35e-02 | 80 |
| hsa0541742 | Liver | HCC | Lipid and atherosclerosis | 118/4020 | 215/8465 | 1.66e-02 | 3.92e-02 | 2.18e-02 | 118 |
| hsa0541752 | Liver | HCC | Lipid and atherosclerosis | 118/4020 | 215/8465 | 1.66e-02 | 3.92e-02 | 2.18e-02 | 118 |
| 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 |
| CYP2C9 | SNV | Missense_Mutation | novel | c.629G>T | p.Ser210Ile | p.S210I | P11712 | protein_coding | deleterious(0.02) | probably_damaging(0.946) | TCGA-A7-A0DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| CYP2C9 | SNV | Missense_Mutation | c.236G>A | p.Gly79Glu | p.G79E | P11712 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CYP2C9 | SNV | Missense_Mutation | c.982N>A | p.Glu328Lys | p.E328K | P11712 | protein_coding | deleterious(0) | benign(0.223) | TCGA-BH-A0B0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR | |
| CYP2C9 | SNV | Missense_Mutation | rs771054349 | c.1372N>G | p.Leu458Val | p.L458V | P11712 | protein_coding | deleterious(0) | possibly_damaging(0.871) | TCGA-BH-A0BZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | CR |
| CYP2C9 | SNV | Missense_Mutation | c.1222N>C | p.Asp408His | p.D408H | P11712 | protein_coding | deleterious(0) | possibly_damaging(0.801) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | |
| CYP2C9 | deletion | Frame_Shift_Del | novel | c.1135delT | p.Tyr379IlefsTer10 | p.Y379Ifs*10 | P11712 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| CYP2C9 | SNV | Missense_Mutation | c.1070G>C | p.Arg357Thr | p.R357T | P11712 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C5-A1BM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CYP2C9 | SNV | Missense_Mutation | c.387G>A | p.Met129Ile | p.M129I | P11712 | protein_coding | deleterious(0.04) | benign(0.08) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| CYP2C9 | SNV | Missense_Mutation | rs200183364 | c.395N>A | p.Arg132Gln | p.R132Q | P11712 | protein_coding | deleterious(0.01) | possibly_damaging(0.481) | TCGA-VS-A8QC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | paclitaxel | PD |
| CYP2C9 | SNV | Missense_Mutation | novel | c.670G>C | p.Asp224His | p.D224H | P11712 | protein_coding | tolerated(0.29) | benign(0.021) | TCGA-VS-A953-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 |
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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 |
| 1559 | CYP2C9 | DRUGGABLE GENOME, ENZYME, CYTOCHROME P450 | CYTARABINE | CYTARABINE | 22931300 | |
| 1559 | CYP2C9 | DRUGGABLE GENOME, ENZYME, CYTOCHROME P450 | CHRYSENE-1,4-DIONE | CHEMBL421215 | ||
| 1559 | CYP2C9 | DRUGGABLE GENOME, ENZYME, CYTOCHROME P450 | GW282974X | GW282974X | ||
| 1559 | CYP2C9 | DRUGGABLE GENOME, ENZYME, CYTOCHROME P450 | PSORALEN | PSORALEN | ||
| 1559 | CYP2C9 | DRUGGABLE GENOME, ENZYME, CYTOCHROME P450 | 6-CHLOROMELATONIN | CHEMBL34730 | ||
| 1559 | CYP2C9 | DRUGGABLE GENOME, ENZYME, CYTOCHROME P450 | MODAFINIL | MODAFINIL | 22931300 | |
| 1559 | CYP2C9 | DRUGGABLE GENOME, ENZYME, CYTOCHROME P450 | CLEMASTINE | CLEMASTINE | 22931300 | |
| 1559 | CYP2C9 | DRUGGABLE GENOME, ENZYME, CYTOCHROME P450 | RO-410960 | CHEMBL1256291 | ||
| 1559 | CYP2C9 | DRUGGABLE GENOME, ENZYME, CYTOCHROME P450 | propofol | PROPOFOL | 24891132 | |
| 1559 | CYP2C9 | DRUGGABLE GENOME, ENZYME, CYTOCHROME P450 | CYCLOSPORINE | CYCLOSPORINE | 22931300 |
| 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 |
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