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Gene: DNPH1 |
Gene summary for DNPH1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | DNPH1 | Gene ID | 10591 |
| Gene name | 2'-deoxynucleoside 5'-phosphate N-hydrolase 1 | |
| Gene Alias | C6orf108 | |
| Cytomap | 6p21.1 | |
| Gene Type | protein-coding | GO ID | GO:0000255 | UniProtAcc | O43598 |
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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 |
| 10591 | DNPH1 | GSM4909281 | Human | Breast | IDC | 4.32e-33 | 7.41e-01 | 0.21 |
| 10591 | DNPH1 | GSM4909282 | Human | Breast | IDC | 1.38e-05 | 3.35e-01 | -0.0288 |
| 10591 | DNPH1 | GSM4909285 | Human | Breast | IDC | 2.02e-05 | 2.48e-01 | 0.21 |
| 10591 | DNPH1 | GSM4909286 | Human | Breast | IDC | 1.56e-10 | 2.04e-01 | 0.1081 |
| 10591 | DNPH1 | GSM4909290 | Human | Breast | IDC | 3.36e-02 | 3.16e-01 | 0.2096 |
| 10591 | DNPH1 | GSM4909291 | Human | Breast | IDC | 2.44e-03 | 3.54e-01 | 0.1753 |
| 10591 | DNPH1 | GSM4909293 | Human | Breast | IDC | 4.82e-02 | 3.73e-02 | 0.1581 |
| 10591 | DNPH1 | GSM4909294 | Human | Breast | IDC | 2.04e-02 | -1.26e-01 | 0.2022 |
| 10591 | DNPH1 | GSM4909297 | Human | Breast | IDC | 8.53e-04 | -9.34e-02 | 0.1517 |
| 10591 | DNPH1 | GSM4909307 | Human | Breast | IDC | 3.68e-20 | 5.75e-01 | 0.1569 |
| 10591 | DNPH1 | GSM4909308 | Human | Breast | IDC | 3.01e-32 | 7.05e-01 | 0.158 |
| 10591 | DNPH1 | GSM4909311 | Human | Breast | IDC | 1.70e-18 | -1.21e-03 | 0.1534 |
| 10591 | DNPH1 | GSM4909312 | Human | Breast | IDC | 4.94e-05 | 1.19e-01 | 0.1552 |
| 10591 | DNPH1 | GSM4909319 | Human | Breast | IDC | 6.16e-25 | -9.50e-02 | 0.1563 |
| 10591 | DNPH1 | GSM4909320 | Human | Breast | IDC | 3.22e-03 | 5.56e-03 | 0.1575 |
| 10591 | DNPH1 | GSM4909321 | Human | Breast | IDC | 2.94e-09 | 1.32e-01 | 0.1559 |
| 10591 | DNPH1 | brca10 | Human | Breast | Precancer | 7.54e-09 | -3.20e-01 | -0.0029 |
| 10591 | DNPH1 | NCCBC11 | Human | Breast | DCIS | 4.46e-03 | 1.36e-01 | 0.1232 |
| 10591 | DNPH1 | NCCBC14 | Human | Breast | DCIS | 1.49e-04 | -4.77e-02 | 0.2021 |
| 10591 | DNPH1 | NCCBC5 | Human | Breast | DCIS | 1.01e-09 | 1.01e-01 | 0.2046 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:00091179 | Breast | Precancer | nucleotide metabolic process | 56/1080 | 489/18723 | 7.40e-07 | 3.00e-05 | 56 |
| GO:00067539 | Breast | Precancer | nucleoside phosphate metabolic process | 56/1080 | 497/18723 | 1.24e-06 | 4.70e-05 | 56 |
| GO:00061639 | Breast | Precancer | purine nucleotide metabolic process | 47/1080 | 396/18723 | 2.14e-06 | 7.50e-05 | 47 |
| GO:00725219 | Breast | Precancer | purine-containing compound metabolic process | 47/1080 | 416/18723 | 8.19e-06 | 2.20e-04 | 47 |
| GO:00346558 | Breast | Precancer | nucleobase-containing compound catabolic process | 42/1080 | 407/18723 | 1.91e-04 | 3.06e-03 | 42 |
| GO:00467007 | Breast | Precancer | heterocycle catabolic process | 44/1080 | 445/18723 | 3.49e-04 | 4.88e-03 | 44 |
| GO:00442708 | Breast | Precancer | cellular nitrogen compound catabolic process | 44/1080 | 451/18723 | 4.64e-04 | 6.12e-03 | 44 |
| GO:00160497 | Breast | Precancer | cell growth | 46/1080 | 482/18723 | 5.63e-04 | 7.16e-03 | 46 |
| GO:00194397 | Breast | Precancer | aromatic compound catabolic process | 44/1080 | 467/18723 | 9.55e-04 | 1.07e-02 | 44 |
| GO:19013617 | Breast | Precancer | organic cyclic compound catabolic process | 45/1080 | 495/18723 | 1.73e-03 | 1.74e-02 | 45 |
| GO:00015587 | Breast | Precancer | regulation of cell growth | 39/1080 | 414/18723 | 1.81e-03 | 1.78e-02 | 39 |
| GO:000675313 | Breast | IDC | nucleoside phosphate metabolic process | 68/1434 | 497/18723 | 2.01e-06 | 8.23e-05 | 68 |
| GO:000911713 | Breast | IDC | nucleotide metabolic process | 67/1434 | 489/18723 | 2.28e-06 | 9.05e-05 | 67 |
| GO:000616314 | Breast | IDC | purine nucleotide metabolic process | 56/1434 | 396/18723 | 5.90e-06 | 1.90e-04 | 56 |
| GO:007252114 | Breast | IDC | purine-containing compound metabolic process | 57/1434 | 416/18723 | 1.28e-05 | 3.31e-04 | 57 |
| GO:001604913 | Breast | IDC | cell growth | 56/1434 | 482/18723 | 1.16e-03 | 1.26e-02 | 56 |
| GO:000155813 | Breast | IDC | regulation of cell growth | 49/1434 | 414/18723 | 1.55e-03 | 1.55e-02 | 49 |
| GO:190136112 | Breast | IDC | organic cyclic compound catabolic process | 56/1434 | 495/18723 | 2.12e-03 | 1.99e-02 | 56 |
| GO:004670012 | Breast | IDC | heterocycle catabolic process | 51/1434 | 445/18723 | 2.51e-03 | 2.25e-02 | 51 |
| GO:003465513 | Breast | IDC | nucleobase-containing compound catabolic process | 47/1434 | 407/18723 | 3.12e-03 | 2.63e-02 | 47 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| DNPH1 | insertion | Frame_Shift_Ins | rs754125969 | c.255_256insAAAGC | p.Gln86LysfsTer11 | p.Q86Kfs*11 | O43598 | protein_coding | TCGA-A8-A091-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | PD | ||
| DNPH1 | SNV | Missense_Mutation | rs763494634 | c.341N>A | p.Arg114Gln | p.R114Q | O43598 | protein_coding | tolerated(0.31) | benign(0.02) | TCGA-C5-A1ML-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| DNPH1 | SNV | Missense_Mutation | novel | c.274G>A | p.Ala92Thr | p.A92T | O43598 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| DNPH1 | SNV | Missense_Mutation | c.221G>T | p.Arg74Met | p.R74M | O43598 | protein_coding | deleterious(0.01) | possibly_damaging(0.564) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| DNPH1 | SNV | Missense_Mutation | rs749012747 | c.416N>A | p.Arg139Gln | p.R139Q | O43598 | protein_coding | tolerated(0.37) | benign(0) | TCGA-B5-A0K6-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| DNPH1 | SNV | Missense_Mutation | c.463G>T | p.Asp155Tyr | p.D155Y | O43598 | protein_coding | deleterious(0) | benign(0.243) | TCGA-G3-A25U-01 | Liver | liver hepatocellular carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| DNPH1 | SNV | Missense_Mutation | c.206N>T | p.Ala69Val | p.A69V | O43598 | protein_coding | tolerated(0.1) | benign(0.045) | TCGA-BR-8363-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| DNPH1 | insertion | Frame_Shift_Ins | novel | c.209_210insAT | p.Gly71LeufsTer25 | p.G71Lfs*25 | O43598 | protein_coding | TCGA-FY-A4B0-01 | Thyroid | thyroid carcinoma | Male | >=65 | I/II | Hormone Therapy | synthroid | SD |
| Page: 1 |
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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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