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Gene: VRK2 |
Gene summary for VRK2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | VRK2 | Gene ID | 7444 |
| Gene name | VRK serine/threonine kinase 2 | |
| Gene Alias | VRK2 | |
| Cytomap | 2p16.1 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q86Y07 |
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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 |
| 7444 | VRK2 | CCI_1 | Human | Cervix | CC | 2.87e-06 | 7.52e-01 | 0.528 |
| 7444 | VRK2 | CCI_2 | Human | Cervix | CC | 1.61e-12 | 1.14e+00 | 0.5249 |
| 7444 | VRK2 | CCI_3 | Human | Cervix | CC | 5.30e-15 | 9.00e-01 | 0.516 |
| 7444 | VRK2 | LZE2T | Human | Esophagus | ESCC | 3.98e-05 | 4.20e-01 | 0.082 |
| 7444 | VRK2 | LZE4T | Human | Esophagus | ESCC | 1.11e-20 | 5.39e-01 | 0.0811 |
| 7444 | VRK2 | LZE7T | Human | Esophagus | ESCC | 5.92e-11 | 6.01e-01 | 0.0667 |
| 7444 | VRK2 | LZE8T | Human | Esophagus | ESCC | 1.52e-05 | 1.77e-01 | 0.067 |
| 7444 | VRK2 | LZE20T | Human | Esophagus | ESCC | 4.64e-04 | 1.94e-01 | 0.0662 |
| 7444 | VRK2 | LZE22T | Human | Esophagus | ESCC | 3.86e-03 | 2.90e-01 | 0.068 |
| 7444 | VRK2 | LZE24T | Human | Esophagus | ESCC | 2.32e-14 | 3.99e-01 | 0.0596 |
| 7444 | VRK2 | LZE21T | Human | Esophagus | ESCC | 1.23e-08 | 4.04e-01 | 0.0655 |
| 7444 | VRK2 | LZE6T | Human | Esophagus | ESCC | 3.97e-07 | 2.51e-01 | 0.0845 |
| 7444 | VRK2 | P1T-E | Human | Esophagus | ESCC | 1.57e-07 | 3.69e-01 | 0.0875 |
| 7444 | VRK2 | P2T-E | Human | Esophagus | ESCC | 3.39e-39 | 6.06e-01 | 0.1177 |
| 7444 | VRK2 | P4T-E | Human | Esophagus | ESCC | 4.55e-17 | 4.19e-01 | 0.1323 |
| 7444 | VRK2 | P5T-E | Human | Esophagus | ESCC | 1.71e-23 | 4.97e-01 | 0.1327 |
| 7444 | VRK2 | P8T-E | Human | Esophagus | ESCC | 2.44e-11 | 3.01e-01 | 0.0889 |
| 7444 | VRK2 | P9T-E | Human | Esophagus | ESCC | 5.63e-18 | 4.33e-01 | 0.1131 |
| 7444 | VRK2 | P10T-E | Human | Esophagus | ESCC | 1.49e-17 | 3.09e-01 | 0.116 |
| 7444 | VRK2 | P11T-E | Human | Esophagus | ESCC | 9.68e-11 | 4.69e-01 | 0.1426 |
| 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 | ||
| 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 |
| ∗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:00705551 | Liver | HCC | response to interleukin-1 | 80/7958 | 143/18723 | 7.95e-04 | 4.77e-03 | 80 |
| GO:00713471 | Liver | HCC | cellular response to interleukin-1 | 61/7958 | 113/18723 | 8.98e-03 | 3.46e-02 | 61 |
| GO:000697920 | Oral cavity | OSCC | response to oxidative stress | 273/7305 | 446/18723 | 8.35e-22 | 1.65e-19 | 273 |
| GO:006219720 | Oral cavity | OSCC | cellular response to chemical stress | 204/7305 | 337/18723 | 6.89e-16 | 5.19e-14 | 204 |
| GO:003459920 | Oral cavity | OSCC | cellular response to oxidative stress | 173/7305 | 288/18723 | 2.90e-13 | 1.43e-11 | 173 |
| GO:00182098 | Oral cavity | OSCC | peptidyl-serine modification | 175/7305 | 338/18723 | 1.09e-06 | 1.46e-05 | 175 |
| GO:001810510 | Oral cavity | OSCC | peptidyl-serine phosphorylation | 164/7305 | 315/18723 | 1.51e-06 | 1.99e-05 | 164 |
| GO:00019594 | Oral cavity | OSCC | regulation of cytokine-mediated signaling pathway | 87/7305 | 150/18723 | 1.82e-06 | 2.35e-05 | 87 |
| GO:00467779 | Oral cavity | OSCC | protein autophosphorylation | 123/7305 | 227/18723 | 2.31e-06 | 2.93e-05 | 123 |
| GO:00607594 | Oral cavity | OSCC | regulation of response to cytokine stimulus | 92/7305 | 162/18723 | 3.25e-06 | 3.90e-05 | 92 |
| GO:00192214 | Oral cavity | OSCC | cytokine-mediated signaling pathway | 222/7305 | 472/18723 | 2.02e-04 | 1.35e-03 | 222 |
| GO:00705556 | Oral cavity | OSCC | response to interleukin-1 | 73/7305 | 143/18723 | 2.23e-03 | 1.00e-02 | 73 |
| GO:00713473 | Oral cavity | OSCC | cellular response to interleukin-1 | 58/7305 | 113/18723 | 5.14e-03 | 2.01e-02 | 58 |
| GO:0006979110 | Oral cavity | LP | response to oxidative stress | 181/4623 | 446/18723 | 5.74e-14 | 6.10e-12 | 181 |
| GO:0062197110 | Oral cavity | LP | cellular response to chemical stress | 130/4623 | 337/18723 | 8.94e-09 | 3.52e-07 | 130 |
| GO:0034599110 | Oral cavity | LP | cellular response to oxidative stress | 110/4623 | 288/18723 | 2.19e-07 | 6.65e-06 | 110 |
| GO:000195911 | Oral cavity | LP | regulation of cytokine-mediated signaling pathway | 58/4623 | 150/18723 | 1.00e-04 | 1.24e-03 | 58 |
| GO:006075911 | Oral cavity | LP | regulation of response to cytokine stimulus | 61/4623 | 162/18723 | 1.61e-04 | 1.81e-03 | 61 |
| GO:001810514 | Oral cavity | EOLP | peptidyl-serine phosphorylation | 84/2218 | 315/18723 | 3.32e-13 | 1.05e-10 | 84 |
| GO:001820914 | Oral cavity | EOLP | peptidyl-serine modification | 87/2218 | 338/18723 | 1.07e-12 | 2.46e-10 | 87 |
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| 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 |
| VRK2 | SNV | Missense_Mutation | c.271N>A | p.Glu91Lys | p.E91K | Q86Y07 | protein_coding | tolerated(1) | benign(0) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| VRK2 | SNV | Missense_Mutation | c.556N>C | p.Asp186His | p.D186H | Q86Y07 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C8-A12T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| VRK2 | SNV | Missense_Mutation | novel | c.946C>A | p.His316Asn | p.H316N | Q86Y07 | protein_coding | tolerated(0.11) | benign(0) | TCGA-PE-A5DC-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| VRK2 | insertion | Nonsense_Mutation | novel | c.833_834insAATACCCCAAA | p.Trp278Ter | p.W278* | Q86Y07 | protein_coding | TCGA-B6-A0IJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| VRK2 | insertion | Frame_Shift_Ins | novel | c.834_835insTGTGATGCTTTGGCAT | p.Ala279CysfsTer14 | p.A279Cfs*14 | Q86Y07 | protein_coding | TCGA-B6-A0IJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| VRK2 | deletion | Frame_Shift_Del | novel | c.614delA | p.Asn205IlefsTer10 | p.N205Ifs*10 | Q86Y07 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| VRK2 | deletion | Frame_Shift_Del | rs768472226 | c.1089delA | p.Val364SerfsTer21 | p.V364Sfs*21 | Q86Y07 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| VRK2 | deletion | Frame_Shift_Del | novel | c.621delN | p.Gly209AlafsTer6 | p.G209Afs*6 | Q86Y07 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| VRK2 | SNV | Missense_Mutation | novel | c.608A>G | p.Gln203Arg | p.Q203R | Q86Y07 | protein_coding | tolerated(0.08) | benign(0.019) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| VRK2 | SNV | Missense_Mutation | novel | c.808N>A | p.Glu270Lys | p.E270K | Q86Y07 | protein_coding | deleterious(0.02) | benign(0.197) | TCGA-ZJ-AAXU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
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