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Gene: DPYD |
Gene summary for DPYD |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | DPYD | Gene ID | 1806 |
| Gene name | dihydropyrimidine dehydrogenase | |
| Gene Alias | DHP | |
| Cytomap | 1p21.3 | |
| Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | Q12882 |
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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 |
| 1806 | DPYD | N_HPV_2 | Human | Cervix | N_HPV | 9.01e-03 | 2.67e-01 | -0.0131 |
| 1806 | DPYD | CCI_1 | Human | Cervix | CC | 9.68e-23 | 2.05e+00 | 0.528 |
| 1806 | DPYD | CCI_2 | Human | Cervix | CC | 3.76e-18 | 1.83e+00 | 0.5249 |
| 1806 | DPYD | CCI_3 | Human | Cervix | CC | 5.70e-19 | 1.54e+00 | 0.516 |
| 1806 | DPYD | LZE8T | Human | Esophagus | ESCC | 2.68e-11 | 3.41e-01 | 0.067 |
| 1806 | DPYD | LZE20T | Human | Esophagus | ESCC | 3.49e-06 | 3.35e-01 | 0.0662 |
| 1806 | DPYD | LZE6T | Human | Esophagus | ESCC | 3.90e-02 | 2.12e-01 | 0.0845 |
| 1806 | DPYD | P1T-E | Human | Esophagus | ESCC | 1.20e-02 | 2.76e-01 | 0.0875 |
| 1806 | DPYD | P2T-E | Human | Esophagus | ESCC | 8.81e-22 | 2.75e-01 | 0.1177 |
| 1806 | DPYD | P5T-E | Human | Esophagus | ESCC | 1.95e-12 | 2.85e-01 | 0.1327 |
| 1806 | DPYD | P8T-E | Human | Esophagus | ESCC | 5.07e-19 | 3.18e-01 | 0.0889 |
| 1806 | DPYD | P9T-E | Human | Esophagus | ESCC | 2.09e-02 | 1.01e-01 | 0.1131 |
| 1806 | DPYD | P11T-E | Human | Esophagus | ESCC | 2.27e-05 | 3.48e-01 | 0.1426 |
| 1806 | DPYD | P12T-E | Human | Esophagus | ESCC | 2.57e-12 | 4.60e-01 | 0.1122 |
| 1806 | DPYD | P15T-E | Human | Esophagus | ESCC | 6.05e-05 | 1.60e-01 | 0.1149 |
| 1806 | DPYD | P16T-E | Human | Esophagus | ESCC | 1.15e-03 | 1.53e-03 | 0.1153 |
| 1806 | DPYD | P17T-E | Human | Esophagus | ESCC | 3.10e-08 | 3.32e-01 | 0.1278 |
| 1806 | DPYD | P19T-E | Human | Esophagus | ESCC | 2.80e-03 | 3.51e-01 | 0.1662 |
| 1806 | DPYD | P20T-E | Human | Esophagus | ESCC | 1.71e-34 | 1.01e+00 | 0.1124 |
| 1806 | DPYD | P23T-E | Human | Esophagus | ESCC | 2.73e-12 | 2.76e-01 | 0.108 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:00160537 | Oral cavity | OSCC | organic acid biosynthetic process | 155/7305 | 316/18723 | 1.64e-04 | 1.13e-03 | 155 |
| GO:00463947 | Oral cavity | OSCC | carboxylic acid biosynthetic process | 154/7305 | 314/18723 | 1.73e-04 | 1.19e-03 | 154 |
| GO:19011361 | Oral cavity | OSCC | carbohydrate derivative catabolic process | 89/7305 | 172/18723 | 4.52e-04 | 2.73e-03 | 89 |
| GO:00091123 | Oral cavity | OSCC | nucleobase metabolic process | 23/7305 | 34/18723 | 6.77e-04 | 3.78e-03 | 23 |
| GO:00091162 | Oral cavity | OSCC | nucleoside metabolic process | 37/7305 | 62/18723 | 7.79e-04 | 4.23e-03 | 37 |
| GO:00463862 | Oral cavity | OSCC | deoxyribose phosphate catabolic process | 21/7305 | 31/18723 | 1.13e-03 | 5.75e-03 | 21 |
| GO:00092192 | Oral cavity | OSCC | pyrimidine deoxyribonucleotide metabolic process | 17/7305 | 24/18723 | 1.59e-03 | 7.56e-03 | 17 |
| GO:00092642 | Oral cavity | OSCC | deoxyribonucleotide catabolic process | 20/7305 | 30/18723 | 1.99e-03 | 9.23e-03 | 20 |
| GO:00442826 | Oral cavity | OSCC | small molecule catabolic process | 174/7305 | 376/18723 | 2.25e-03 | 1.00e-02 | 174 |
| GO:00086524 | Oral cavity | OSCC | cellular amino acid biosynthetic process | 42/7305 | 76/18723 | 2.93e-03 | 1.27e-02 | 42 |
| GO:00725272 | Oral cavity | OSCC | pyrimidine-containing compound metabolic process | 44/7305 | 82/18723 | 4.95e-03 | 1.94e-02 | 44 |
| GO:00061443 | Oral cavity | OSCC | purine nucleobase metabolic process | 13/7305 | 19/18723 | 9.07e-03 | 3.26e-02 | 13 |
| GO:00062063 | Oral cavity | OSCC | pyrimidine nucleobase metabolic process | 11/7305 | 16/18723 | 1.56e-02 | 4.99e-02 | 11 |
| GO:003465523 | Oral cavity | EOLP | nucleobase-containing compound catabolic process | 89/2218 | 407/18723 | 5.47e-09 | 2.92e-07 | 89 |
| GO:004670023 | Oral cavity | EOLP | heterocycle catabolic process | 93/2218 | 445/18723 | 2.61e-08 | 1.08e-06 | 93 |
| GO:004427023 | Oral cavity | EOLP | cellular nitrogen compound catabolic process | 92/2218 | 451/18723 | 1.01e-07 | 3.45e-06 | 92 |
| GO:001943923 | Oral cavity | EOLP | aromatic compound catabolic process | 92/2218 | 467/18723 | 5.23e-07 | 1.40e-05 | 92 |
| GO:190136123 | Oral cavity | EOLP | organic cyclic compound catabolic process | 95/2218 | 495/18723 | 1.15e-06 | 2.80e-05 | 95 |
| GO:003465531 | Oral cavity | NEOLP | nucleobase-containing compound catabolic process | 73/2005 | 407/18723 | 6.69e-06 | 1.34e-04 | 73 |
| GO:004670031 | Oral cavity | NEOLP | heterocycle catabolic process | 75/2005 | 445/18723 | 4.61e-05 | 6.38e-04 | 75 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa002405 | Esophagus | ESCC | Pyrimidine metabolism | 41/4205 | 58/8465 | 9.14e-04 | 2.92e-03 | 1.49e-03 | 41 |
| hsa0024012 | Esophagus | ESCC | Pyrimidine metabolism | 41/4205 | 58/8465 | 9.14e-04 | 2.92e-03 | 1.49e-03 | 41 |
| 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 |
| hsa002402 | Liver | HCC | Pyrimidine metabolism | 44/4020 | 58/8465 | 9.34e-06 | 7.11e-05 | 3.95e-05 | 44 |
| hsa009832 | Liver | HCC | Drug metabolism - other enzymes | 54/4020 | 80/8465 | 2.25e-04 | 1.09e-03 | 6.08e-04 | 54 |
| hsa004102 | Liver | HCC | beta-Alanine metabolism | 22/4020 | 31/8465 | 6.93e-03 | 1.92e-02 | 1.07e-02 | 22 |
| hsa007702 | Liver | HCC | Pantothenate and CoA biosynthesis | 16/4020 | 21/8465 | 7.16e-03 | 1.97e-02 | 1.09e-02 | 16 |
| hsa002403 | Liver | HCC | Pyrimidine metabolism | 44/4020 | 58/8465 | 9.34e-06 | 7.11e-05 | 3.95e-05 | 44 |
| hsa009833 | Liver | HCC | Drug metabolism - other enzymes | 54/4020 | 80/8465 | 2.25e-04 | 1.09e-03 | 6.08e-04 | 54 |
| hsa004103 | Liver | HCC | beta-Alanine metabolism | 22/4020 | 31/8465 | 6.93e-03 | 1.92e-02 | 1.07e-02 | 22 |
| hsa007703 | Liver | HCC | Pantothenate and CoA biosynthesis | 16/4020 | 21/8465 | 7.16e-03 | 1.97e-02 | 1.09e-02 | 16 |
| hsa002404 | Oral cavity | OSCC | Pyrimidine metabolism | 37/3704 | 58/8465 | 1.62e-03 | 4.45e-03 | 2.26e-03 | 37 |
| hsa0024011 | Oral cavity | OSCC | Pyrimidine metabolism | 37/3704 | 58/8465 | 1.62e-03 | 4.45e-03 | 2.26e-03 | 37 |
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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 |
| DPYD | SNV | Missense_Mutation | novel | c.1714C>T | p.Leu572Phe | p.L572F | Q12882 | protein_coding | deleterious(0) | possibly_damaging(0.68) | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| DPYD | SNV | Missense_Mutation | novel | c.1982N>C | p.Gly661Ala | p.G661A | Q12882 | protein_coding | deleterious(0) | probably_damaging(0.963) | TCGA-BH-A0H5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
| DPYD | SNV | Missense_Mutation | novel | c.1756N>T | p.Val586Phe | p.V586F | Q12882 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-OL-A5DA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| DPYD | SNV | Missense_Mutation | novel | c.827A>G | p.Tyr276Cys | p.Y276C | Q12882 | protein_coding | deleterious(0.03) | benign(0.132) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| DPYD | SNV | Missense_Mutation | c.1822C>G | p.Leu608Val | p.L608V | Q12882 | protein_coding | tolerated(0.35) | possibly_damaging(0.688) | TCGA-C5-A8XH-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| DPYD | SNV | Missense_Mutation | novel | c.838T>G | p.Phe280Val | p.F280V | Q12882 | protein_coding | deleterious(0) | possibly_damaging(0.892) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| DPYD | SNV | Missense_Mutation | rs763862486 | c.2848N>A | p.Glu950Lys | p.E950K | Q12882 | protein_coding | tolerated(0.11) | possibly_damaging(0.593) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| DPYD | SNV | Missense_Mutation | novel | c.1147N>A | p.Glu383Lys | p.E383K | Q12882 | protein_coding | deleterious(0.03) | benign(0.068) | TCGA-MA-AA3Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| DPYD | SNV | Missense_Mutation | c.1010T>C | p.Val337Ala | p.V337A | Q12882 | protein_coding | deleterious(0) | possibly_damaging(0.891) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| DPYD | SNV | Missense_Mutation | c.3023N>A | p.Thr1008Lys | p.T1008K | Q12882 | protein_coding | tolerated(0.87) | benign(0) | TCGA-A6-6649-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
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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 |
| 1806 | DPYD | ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | Capecitabine | CAPECITABINE | ||
| 1806 | DPYD | ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | tegafur | TEGAFUR | 12209976,28950804,24923815,30858516,23603345,16115930,27122156,31382864,22490566,9470816,18600527,15944764,26603945,18443386,17700593,17165084,17000685,19530960,26794347,19795123,12360106,19473056,9439663,26099996,26216193,27864592,17121937,18299612,28295243,15132136,20819423,27995989,16151913,15017333,24817302,30114658,29846282,9323575,29134491,23988873,17203168,11895907,32378051,25677447,17064846,20385995,25796495,26265035,17417073,30723313,17848752,23930673,20665215,26804652,28929491,11350878,11555601,23942539,18452418,27454530,25410891,16361556,21077799,10803677,29889674,14635116,11156223,26846104,21498394,19858398,10071185,23585145 | |
| 1806 | DPYD | ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | Eniluracil | ENILURACIL | ||
| 1806 | DPYD | ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | s 1 (combination) | 24923815,30858516,16115930,22490566,19530960,26794347,19473056,29845393,26099996,26216193,18299612,20819423,30114658,28614820,11895907,25677447,26265035,30723313,26804652,29239269,25410891,10803677,14635116,11156223,26846104,21498394 | ||
| 1806 | DPYD | ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | Pyrimidine analogues | 12209976,28950804,24923815,30858516,23603345,16115930,27122156,31382864,22490566,9470816,18600527,26603945,18443386,17700593,17165084,17000685,19530960,26794347,19795123,12360106,19473056,9439663,29845393,26099996,26216193,27864592,17121937,18299612,28295243,15132136,20819423,27995989,16151913,15017333,24817302,30114658,29846282,9323575,29134491,17203168,11895907,32378051,25677447,17064846,20385995,25796495,26265035,17417073,30723313,17848752,23930673,20665215,26804652,29239269,28929491,11350878,11555601,23942539,18452418,27454530,25410891,16361556,21077799,10803677,29889674,14635116,11156223,26846104,21498394,19858398,10071185,23585145 | ||
| 1806 | DPYD | ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | 5-FU | FLUOROURACIL | 16421754,15538739,11501504 | |
| 1806 | DPYD | ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | irinotecan | IRINOTECAN | 28395759 | |
| 1806 | DPYD | ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | LEUCOVORIN | LEUCOVORIN | 11977552,12576451 | |
| 1806 | DPYD | ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | leucovorin | LEUCOVORIN | ||
| 1806 | DPYD | ENZYME, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | flucytosine | FLUCYTOSINE |
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