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Gene: DKK3 |
Gene summary for DKK3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | DKK3 | Gene ID | 27122 |
| Gene name | dickkopf WNT signaling pathway inhibitor 3 | |
| Gene Alias | REIC | |
| Cytomap | 11p15.3 | |
| Gene Type | protein-coding | GO ID | GO:0006066 | UniProtAcc | Q9UBP4 |
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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 |
| 27122 | DKK3 | LZE4T | Human | Esophagus | ESCC | 8.94e-07 | 1.83e-01 | 0.0811 |
| 27122 | DKK3 | LZE8T | Human | Esophagus | ESCC | 1.99e-05 | -2.66e-01 | 0.067 |
| 27122 | DKK3 | LZE24T | Human | Esophagus | ESCC | 9.31e-07 | -1.14e-01 | 0.0596 |
| 27122 | DKK3 | LZE6T | Human | Esophagus | ESCC | 8.31e-04 | -2.51e-01 | 0.0845 |
| 27122 | DKK3 | P2T-E | Human | Esophagus | ESCC | 2.30e-50 | 1.21e+00 | 0.1177 |
| 27122 | DKK3 | P4T-E | Human | Esophagus | ESCC | 3.69e-15 | 5.47e-01 | 0.1323 |
| 27122 | DKK3 | P8T-E | Human | Esophagus | ESCC | 5.45e-08 | 4.31e-01 | 0.0889 |
| 27122 | DKK3 | P9T-E | Human | Esophagus | ESCC | 1.03e-05 | 5.31e-01 | 0.1131 |
| 27122 | DKK3 | P10T-E | Human | Esophagus | ESCC | 5.50e-58 | 1.45e+00 | 0.116 |
| 27122 | DKK3 | P11T-E | Human | Esophagus | ESCC | 4.17e-35 | 2.18e+00 | 0.1426 |
| 27122 | DKK3 | P12T-E | Human | Esophagus | ESCC | 2.62e-21 | 6.75e-01 | 0.1122 |
| 27122 | DKK3 | P15T-E | Human | Esophagus | ESCC | 2.36e-14 | 8.77e-01 | 0.1149 |
| 27122 | DKK3 | P16T-E | Human | Esophagus | ESCC | 9.93e-44 | 1.27e+00 | 0.1153 |
| 27122 | DKK3 | P17T-E | Human | Esophagus | ESCC | 5.39e-07 | 1.04e+00 | 0.1278 |
| 27122 | DKK3 | P20T-E | Human | Esophagus | ESCC | 1.12e-16 | 8.41e-01 | 0.1124 |
| 27122 | DKK3 | P21T-E | Human | Esophagus | ESCC | 3.67e-62 | 1.61e+00 | 0.1617 |
| 27122 | DKK3 | P22T-E | Human | Esophagus | ESCC | 1.20e-54 | 1.21e+00 | 0.1236 |
| 27122 | DKK3 | P24T-E | Human | Esophagus | ESCC | 1.05e-17 | 7.66e-01 | 0.1287 |
| 27122 | DKK3 | P26T-E | Human | Esophagus | ESCC | 2.40e-93 | 1.92e+00 | 0.1276 |
| 27122 | DKK3 | P27T-E | Human | Esophagus | ESCC | 2.48e-41 | 1.16e+00 | 0.1055 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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:0048732111 | Esophagus | ESCC | gland development | 269/8552 | 436/18723 | 7.81e-12 | 2.95e-10 | 269 |
| GO:001605517 | Esophagus | ESCC | Wnt signaling pathway | 268/8552 | 444/18723 | 2.32e-10 | 6.58e-09 | 268 |
| GO:019873817 | Esophagus | ESCC | cell-cell signaling by wnt | 269/8552 | 446/18723 | 2.41e-10 | 6.79e-09 | 269 |
| GO:00715599 | Esophagus | ESCC | response to transforming growth factor beta | 157/8552 | 256/18723 | 2.95e-07 | 4.23e-06 | 157 |
| GO:003011117 | Esophagus | ESCC | regulation of Wnt signaling pathway | 194/8552 | 328/18723 | 5.39e-07 | 7.14e-06 | 194 |
| GO:006007016 | Esophagus | ESCC | canonical Wnt signaling pathway | 180/8552 | 303/18723 | 9.15e-07 | 1.17e-05 | 180 |
| GO:006082817 | Esophagus | ESCC | regulation of canonical Wnt signaling pathway | 153/8552 | 253/18723 | 1.38e-06 | 1.67e-05 | 153 |
| GO:00715609 | Esophagus | ESCC | cellular response to transforming growth factor beta stimulus | 151/8552 | 250/18723 | 1.78e-06 | 2.10e-05 | 151 |
| GO:00060668 | Esophagus | ESCC | alcohol metabolic process | 202/8552 | 353/18723 | 7.32e-06 | 7.26e-05 | 202 |
| GO:00071799 | Esophagus | ESCC | transforming growth factor beta receptor signaling pathway | 121/8552 | 198/18723 | 8.26e-06 | 8.03e-05 | 121 |
| GO:000717810 | Esophagus | ESCC | transmembrane receptor protein serine/threonine kinase signaling pathway | 195/8552 | 355/18723 | 2.58e-04 | 1.58e-03 | 195 |
| GO:00620129 | Esophagus | ESCC | regulation of small molecule metabolic process | 184/8552 | 334/18723 | 3.11e-04 | 1.85e-03 | 184 |
| GO:00421805 | Esophagus | ESCC | cellular ketone metabolic process | 120/8552 | 211/18723 | 6.70e-04 | 3.55e-03 | 120 |
| GO:00461653 | Esophagus | ESCC | alcohol biosynthetic process | 83/8552 | 140/18723 | 8.04e-04 | 4.16e-03 | 83 |
| GO:00060818 | Esophagus | ESCC | cellular aldehyde metabolic process | 40/8552 | 60/18723 | 8.30e-04 | 4.28e-03 | 40 |
| GO:00301788 | Esophagus | ESCC | negative regulation of Wnt signaling pathway | 97/8552 | 170/18723 | 1.81e-03 | 8.31e-03 | 97 |
| GO:00170156 | Esophagus | ESCC | regulation of transforming growth factor beta receptor signaling pathway | 75/8552 | 128/18723 | 2.19e-03 | 9.71e-03 | 75 |
| GO:00066946 | Esophagus | ESCC | steroid biosynthetic process | 98/8552 | 173/18723 | 2.34e-03 | 1.03e-02 | 98 |
| GO:19038447 | Esophagus | ESCC | regulation of cellular response to transforming growth factor beta stimulus | 76/8552 | 131/18723 | 2.96e-03 | 1.24e-02 | 76 |
| GO:00900905 | Esophagus | ESCC | negative regulation of canonical Wnt signaling pathway | 78/8552 | 137/18723 | 5.17e-03 | 1.95e-02 | 78 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 |
| DKK3 | SNV | Missense_Mutation | c.566N>A | p.Leu189Gln | p.L189Q | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| DKK3 | SNV | Missense_Mutation | novel | c.695C>A | p.Thr232Lys | p.T232K | protein_coding | deleterious(0.02) | possibly_damaging(0.763) | TCGA-B6-A400-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| DKK3 | SNV | Missense_Mutation | c.278G>A | p.Ser93Asn | p.S93N | protein_coding | tolerated(1) | benign(0.001) | TCGA-E2-A14R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD | ||
| DKK3 | SNV | Missense_Mutation | rs373767107 | c.907N>A | p.Val303Met | p.V303M | protein_coding | tolerated_low_confidence(0.15) | benign(0.01) | TCGA-OL-A97C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| DKK3 | SNV | Missense_Mutation | novel | c.440N>A | p.Cys147Tyr | p.C147Y | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| DKK3 | SNV | Missense_Mutation | novel | c.221N>G | p.Ala74Gly | p.A74G | protein_coding | tolerated(0.05) | probably_damaging(0.996) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| DKK3 | SNV | Missense_Mutation | c.182C>T | p.Thr61Met | p.T61M | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| DKK3 | SNV | Missense_Mutation | rs377759604 | c.514C>T | p.Arg172Trp | p.R172W | protein_coding | deleterious(0.02) | probably_damaging(0.971) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| DKK3 | SNV | Missense_Mutation | c.439N>C | p.Cys147Arg | p.C147R | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | ||
| DKK3 | SNV | Missense_Mutation | rs756280059 | c.995N>A | p.Arg332His | p.R332H | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.973) | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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 |
| 27122 | DKK3 | DRUGGABLE GENOME | REIC gene therapy |
| Page: 1 |
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