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Gene: DKC1 |
Gene summary for DKC1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | DKC1 | Gene ID | 1736 |
| Gene name | dyskerin pseudouridine synthase 1 | |
| Gene Alias | CBF5 | |
| Cytomap | Xq28 | |
| Gene Type | protein-coding | GO ID | GO:0000154 | UniProtAcc | O60832 |
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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 |
| 1736 | DKC1 | HTA11_347_2000001011 | Human | Colorectum | AD | 9.96e-03 | 1.84e-01 | -0.1954 |
| 1736 | DKC1 | HTA11_866_3004761011 | Human | Colorectum | AD | 7.79e-07 | 3.59e-01 | 0.096 |
| 1736 | DKC1 | HTA11_6801_2000001011 | Human | Colorectum | SER | 5.38e-03 | 5.14e-01 | 0.0171 |
| 1736 | DKC1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 5.16e-11 | 4.89e-01 | 0.0674 |
| 1736 | DKC1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 6.59e-15 | 5.73e-01 | 0.294 |
| 1736 | DKC1 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.91e-03 | 9.73e-01 | 0.3487 |
| 1736 | DKC1 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.17e-25 | 1.03e+00 | 0.281 |
| 1736 | DKC1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.40e-28 | 9.20e-01 | 0.3859 |
| 1736 | DKC1 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 2.29e-10 | 7.75e-01 | 0.2585 |
| 1736 | DKC1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.44e-15 | 5.49e-01 | 0.3005 |
| 1736 | DKC1 | LZE2T | Human | Esophagus | ESCC | 1.88e-08 | 1.62e+00 | 0.082 |
| 1736 | DKC1 | LZE4T | Human | Esophagus | ESCC | 6.82e-05 | 2.33e-01 | 0.0811 |
| 1736 | DKC1 | LZE7T | Human | Esophagus | ESCC | 1.21e-11 | 9.42e-01 | 0.0667 |
| 1736 | DKC1 | LZE22D1 | Human | Esophagus | HGIN | 6.55e-04 | -8.88e-02 | 0.0595 |
| 1736 | DKC1 | LZE22T | Human | Esophagus | ESCC | 3.70e-02 | 5.66e-01 | 0.068 |
| 1736 | DKC1 | LZE24T | Human | Esophagus | ESCC | 6.71e-21 | 7.22e-01 | 0.0596 |
| 1736 | DKC1 | LZE6T | Human | Esophagus | ESCC | 4.61e-02 | 2.89e-01 | 0.0845 |
| 1736 | DKC1 | P1T-E | Human | Esophagus | ESCC | 1.57e-04 | 7.11e-01 | 0.0875 |
| 1736 | DKC1 | P2T-E | Human | Esophagus | ESCC | 8.65e-34 | 9.79e-01 | 0.1177 |
| 1736 | DKC1 | P4T-E | Human | Esophagus | ESCC | 1.32e-28 | 9.07e-01 | 0.1323 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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 | ||
| 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:0009895 | Colorectum | AD | negative regulation of catabolic process | 124/3918 | 320/18723 | 1.66e-13 | 3.35e-11 | 124 |
| GO:1903829 | Colorectum | AD | positive regulation of cellular protein localization | 110/3918 | 276/18723 | 4.58e-13 | 8.44e-11 | 110 |
| GO:0031330 | Colorectum | AD | negative regulation of cellular catabolic process | 104/3918 | 262/18723 | 2.66e-12 | 3.96e-10 | 104 |
| GO:0072594 | Colorectum | AD | establishment of protein localization to organelle | 148/3918 | 422/18723 | 7.95e-12 | 1.04e-09 | 148 |
| GO:0006401 | Colorectum | AD | RNA catabolic process | 102/3918 | 278/18723 | 8.64e-10 | 6.76e-08 | 102 |
| GO:0022613 | Colorectum | AD | ribonucleoprotein complex biogenesis | 151/3918 | 463/18723 | 1.96e-09 | 1.39e-07 | 151 |
| GO:1904951 | Colorectum | AD | positive regulation of establishment of protein localization | 112/3918 | 319/18723 | 2.55e-09 | 1.80e-07 | 112 |
| GO:0044270 | Colorectum | AD | cellular nitrogen compound catabolic process | 147/3918 | 451/18723 | 3.35e-09 | 2.23e-07 | 147 |
| GO:0046700 | Colorectum | AD | heterocycle catabolic process | 145/3918 | 445/18723 | 4.37e-09 | 2.84e-07 | 145 |
| GO:0034655 | Colorectum | AD | nucleobase-containing compound catabolic process | 133/3918 | 407/18723 | 1.56e-08 | 9.12e-07 | 133 |
| GO:0019439 | Colorectum | AD | aromatic compound catabolic process | 146/3918 | 467/18723 | 7.48e-08 | 3.84e-06 | 146 |
| GO:1901361 | Colorectum | AD | organic cyclic compound catabolic process | 153/3918 | 495/18723 | 8.23e-08 | 4.18e-06 | 153 |
| GO:1900180 | Colorectum | AD | regulation of protein localization to nucleus | 55/3918 | 136/18723 | 1.70e-07 | 7.34e-06 | 55 |
| GO:0051052 | Colorectum | AD | regulation of DNA metabolic process | 116/3918 | 359/18723 | 2.47e-07 | 1.00e-05 | 116 |
| GO:0051054 | Colorectum | AD | positive regulation of DNA metabolic process | 73/3918 | 201/18723 | 3.27e-07 | 1.29e-05 | 73 |
| GO:0043487 | Colorectum | AD | regulation of RNA stability | 63/3918 | 170/18723 | 9.17e-07 | 3.12e-05 | 63 |
| GO:1900182 | Colorectum | AD | positive regulation of protein localization to nucleus | 38/3918 | 87/18723 | 1.43e-06 | 4.52e-05 | 38 |
| GO:0006403 | Colorectum | AD | RNA localization | 71/3918 | 201/18723 | 1.54e-06 | 4.76e-05 | 71 |
| GO:0034504 | Colorectum | AD | protein localization to nucleus | 94/3918 | 290/18723 | 2.83e-06 | 8.09e-05 | 94 |
| GO:2001252 | Colorectum | AD | positive regulation of chromosome organization | 35/3918 | 82/18723 | 6.90e-06 | 1.72e-04 | 35 |
| 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 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| DKC1 | SNV | Missense_Mutation | novel | c.601G>A | p.Glu201Lys | p.E201K | O60832 | protein_coding | deleterious(0.03) | benign(0.094) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| DKC1 | SNV | Missense_Mutation | c.58N>G | p.Lys20Glu | p.K20E | O60832 | protein_coding | deleterious_low_confidence(0.02) | benign(0.196) | TCGA-AR-A0TW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | PD | |
| DKC1 | SNV | Missense_Mutation | c.39N>G | p.His13Gln | p.H13Q | O60832 | protein_coding | tolerated_low_confidence(0.12) | benign(0.048) | TCGA-AR-A24H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| DKC1 | insertion | Frame_Shift_Ins | novel | c.558_559insCTACTCGGGAGGCTGAGGCAGGAGA | p.Ile187LeufsTer28 | p.I187Lfs*28 | O60832 | protein_coding | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| DKC1 | SNV | Missense_Mutation | c.1378N>T | p.Pro460Ser | p.P460S | O60832 | protein_coding | tolerated_low_confidence(0.11) | benign(0) | TCGA-C5-A1BJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| DKC1 | SNV | Missense_Mutation | novel | c.89N>C | p.Ile30Thr | p.I30T | O60832 | protein_coding | tolerated(0.14) | benign(0.017) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| DKC1 | SNV | Missense_Mutation | c.763N>G | p.Ser255Gly | p.S255G | O60832 | protein_coding | tolerated(0.61) | benign(0.009) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| DKC1 | SNV | Missense_Mutation | c.1106T>C | p.Val369Ala | p.V369A | O60832 | protein_coding | deleterious(0.01) | probably_damaging(0.942) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| DKC1 | SNV | Missense_Mutation | rs782117503 | c.1334N>T | p.Ala445Val | p.A445V | O60832 | protein_coding | tolerated(0.46) | benign(0) | TCGA-CM-5861-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| DKC1 | SNV | Missense_Mutation | rs782010351 | c.55N>T | p.Arg19Trp | p.R19W | O60832 | protein_coding | deleterious_low_confidence(0) | benign(0.249) | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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 |
| 1736 | DKC1 | CLINICALLY ACTIONABLE | V934/V935 |
| Page: 1 |
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