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Gene: PMVK |
Gene summary for PMVK |
Gene summary. |
Gene information | Species | Human | Gene symbol | PMVK | Gene ID | 10654 |
Gene name | phosphomevalonate kinase | |
Gene Alias | HUMPMKI | |
Cytomap | 1q21.3 | |
Gene Type | protein-coding | GO ID | GO:0006066 | UniProtAcc | Q6FGV9 |
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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 |
10654 | PMVK | P89T-E | Human | Esophagus | ESCC | 2.90e-11 | 1.10e+00 | 0.1752 |
10654 | PMVK | P91T-E | Human | Esophagus | ESCC | 3.70e-10 | 1.57e+00 | 0.1828 |
10654 | PMVK | P107T-E | Human | Esophagus | ESCC | 5.03e-39 | 1.01e+00 | 0.171 |
10654 | PMVK | P126T-E | Human | Esophagus | ESCC | 2.61e-06 | 9.09e-01 | 0.1125 |
10654 | PMVK | P127T-E | Human | Esophagus | ESCC | 8.49e-14 | 2.42e-01 | 0.0826 |
10654 | PMVK | P128T-E | Human | Esophagus | ESCC | 2.24e-29 | 1.01e+00 | 0.1241 |
10654 | PMVK | P130T-E | Human | Esophagus | ESCC | 2.45e-94 | 2.17e+00 | 0.1676 |
10654 | PMVK | S43 | Human | Liver | Cirrhotic | 3.20e-06 | -2.27e-01 | -0.0187 |
10654 | PMVK | HCC1_Meng | Human | Liver | HCC | 1.67e-70 | 2.28e-01 | 0.0246 |
10654 | PMVK | HCC2_Meng | Human | Liver | HCC | 5.07e-30 | 9.67e-02 | 0.0107 |
10654 | PMVK | cirrhotic1 | Human | Liver | Cirrhotic | 4.12e-05 | 1.80e-01 | 0.0202 |
10654 | PMVK | cirrhotic2 | Human | Liver | Cirrhotic | 3.76e-03 | 1.48e-01 | 0.0201 |
10654 | PMVK | cirrhotic3 | Human | Liver | Cirrhotic | 4.56e-11 | 1.65e-01 | 0.0215 |
10654 | PMVK | HCC1 | Human | Liver | HCC | 1.84e-02 | 1.66e+00 | 0.5336 |
10654 | PMVK | HCC2 | Human | Liver | HCC | 2.76e-10 | 3.86e+00 | 0.5341 |
10654 | PMVK | Pt13.b | Human | Liver | HCC | 1.42e-23 | 2.74e-01 | 0.0251 |
10654 | PMVK | Pt14.a | Human | Liver | HCC | 1.42e-07 | 4.07e-01 | 0.0169 |
10654 | PMVK | Pt14.b | Human | Liver | HCC | 1.96e-07 | 3.51e-01 | 0.018 |
10654 | PMVK | Pt14.d | Human | Liver | HCC | 9.25e-04 | 2.66e-01 | 0.0143 |
10654 | PMVK | S014 | Human | Liver | HCC | 2.39e-30 | 1.28e+00 | 0.2254 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:000915014 | Breast | IDC | purine ribonucleotide metabolic process | 55/1434 | 368/18723 | 1.30e-06 | 5.72e-05 | 55 |
GO:001969314 | Breast | IDC | ribose phosphate metabolic process | 58/1434 | 396/18723 | 1.31e-06 | 5.73e-05 | 58 |
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:000925914 | Breast | IDC | ribonucleotide metabolic process | 56/1434 | 385/18723 | 2.47e-06 | 9.63e-05 | 56 |
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:009730514 | Breast | IDC | response to alcohol | 36/1434 | 253/18723 | 2.29e-04 | 3.64e-03 | 36 |
GO:00066944 | Breast | IDC | steroid biosynthetic process | 25/1434 | 173/18723 | 1.56e-03 | 1.56e-02 | 25 |
GO:001969324 | Breast | DCIS | ribose phosphate metabolic process | 58/1390 | 396/18723 | 4.80e-07 | 2.11e-05 | 58 |
GO:000915024 | Breast | DCIS | purine ribonucleotide metabolic process | 55/1390 | 368/18723 | 4.92e-07 | 2.14e-05 | 55 |
GO:000925924 | Breast | DCIS | ribonucleotide metabolic process | 56/1390 | 385/18723 | 9.44e-07 | 3.79e-05 | 56 |
GO:000616324 | Breast | DCIS | purine nucleotide metabolic process | 56/1390 | 396/18723 | 2.31e-06 | 8.29e-05 | 56 |
GO:000911723 | Breast | DCIS | nucleotide metabolic process | 65/1390 | 489/18723 | 3.19e-06 | 1.03e-04 | 65 |
GO:007252124 | Breast | DCIS | purine-containing compound metabolic process | 57/1390 | 416/18723 | 5.07e-06 | 1.48e-04 | 57 |
GO:000675323 | Breast | DCIS | nucleoside phosphate metabolic process | 65/1390 | 497/18723 | 5.51e-06 | 1.59e-04 | 65 |
GO:009730524 | Breast | DCIS | response to alcohol | 34/1390 | 253/18723 | 5.54e-04 | 7.09e-03 | 34 |
GO:000669411 | Breast | DCIS | steroid biosynthetic process | 23/1390 | 173/18723 | 4.63e-03 | 3.52e-02 | 23 |
GO:00086544 | Esophagus | ESCC | phospholipid biosynthetic process | 162/8552 | 253/18723 | 2.59e-09 | 5.73e-08 | 162 |
GO:0006753110 | Esophagus | ESCC | nucleoside phosphate metabolic process | 288/8552 | 497/18723 | 1.80e-08 | 3.50e-07 | 288 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa009005 | Esophagus | ESCC | Terpenoid backbone biosynthesis | 20/4205 | 23/8465 | 2.14e-04 | 7.87e-04 | 4.03e-04 | 20 |
hsa041467 | Esophagus | ESCC | Peroxisome | 55/4205 | 82/8465 | 1.04e-03 | 3.27e-03 | 1.68e-03 | 55 |
hsa0090012 | Esophagus | ESCC | Terpenoid backbone biosynthesis | 20/4205 | 23/8465 | 2.14e-04 | 7.87e-04 | 4.03e-04 | 20 |
hsa0414612 | Esophagus | ESCC | Peroxisome | 55/4205 | 82/8465 | 1.04e-03 | 3.27e-03 | 1.68e-03 | 55 |
hsa041462 | Liver | Cirrhotic | Peroxisome | 36/2530 | 82/8465 | 4.79e-03 | 1.74e-02 | 1.07e-02 | 36 |
hsa041463 | Liver | Cirrhotic | Peroxisome | 36/2530 | 82/8465 | 4.79e-03 | 1.74e-02 | 1.07e-02 | 36 |
hsa041464 | Liver | HCC | Peroxisome | 58/4020 | 82/8465 | 1.57e-05 | 1.05e-04 | 5.85e-05 | 58 |
hsa00900 | Liver | HCC | Terpenoid backbone biosynthesis | 17/4020 | 23/8465 | 9.26e-03 | 2.46e-02 | 1.37e-02 | 17 |
hsa041465 | Liver | HCC | Peroxisome | 58/4020 | 82/8465 | 1.57e-05 | 1.05e-04 | 5.85e-05 | 58 |
hsa009001 | Liver | HCC | Terpenoid backbone biosynthesis | 17/4020 | 23/8465 | 9.26e-03 | 2.46e-02 | 1.37e-02 | 17 |
hsa009004 | Oral cavity | OSCC | Terpenoid backbone biosynthesis | 19/3704 | 23/8465 | 1.55e-04 | 5.34e-04 | 2.72e-04 | 19 |
hsa041466 | Oral cavity | OSCC | Peroxisome | 47/3704 | 82/8465 | 9.01e-03 | 2.01e-02 | 1.03e-02 | 47 |
hsa0090011 | Oral cavity | OSCC | Terpenoid backbone biosynthesis | 19/3704 | 23/8465 | 1.55e-04 | 5.34e-04 | 2.72e-04 | 19 |
hsa0414611 | Oral cavity | OSCC | Peroxisome | 47/3704 | 82/8465 | 9.01e-03 | 2.01e-02 | 1.03e-02 | 47 |
hsa009002 | Oral cavity | LP | Terpenoid backbone biosynthesis | 12/2418 | 23/8465 | 1.43e-02 | 4.59e-02 | 2.96e-02 | 12 |
hsa0414621 | Oral cavity | LP | Peroxisome | 33/2418 | 82/8465 | 1.48e-02 | 4.69e-02 | 3.03e-02 | 33 |
hsa009003 | Oral cavity | LP | Terpenoid backbone biosynthesis | 12/2418 | 23/8465 | 1.43e-02 | 4.59e-02 | 2.96e-02 | 12 |
hsa0414631 | Oral cavity | LP | Peroxisome | 33/2418 | 82/8465 | 1.48e-02 | 4.69e-02 | 3.03e-02 | 33 |
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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 |
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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. |
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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 |
PMVK | SNV | Missense_Mutation | c.547N>T | p.Asn183Tyr | p.N183Y | Q15126 | protein_coding | deleterious(0.03) | benign(0.021) | TCGA-GM-A2DC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | xeloda | CR | |
PMVK | insertion | Nonsense_Mutation | novel | c.277_278insACGAGTCATAAGGTTTGTAAAGAAGTCGATTAGGGGCTGGGGT | p.Arg93AsnfsTer4 | p.R93Nfs*4 | Q15126 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
PMVK | SNV | Missense_Mutation | c.158N>T | p.Gln53Leu | p.Q53L | Q15126 | protein_coding | tolerated(0.07) | benign(0.001) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
PMVK | SNV | Missense_Mutation | rs775004187 | c.293G>A | p.Gly98Asp | p.G98D | Q15126 | protein_coding | tolerated(0.13) | benign(0.107) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
PMVK | SNV | Missense_Mutation | rs779946272 | c.398N>T | p.Ala133Val | p.A133V | Q15126 | protein_coding | deleterious(0.05) | benign(0.211) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
PMVK | SNV | Missense_Mutation | novel | c.190N>T | p.Asp64Tyr | p.D64Y | Q15126 | protein_coding | deleterious(0.01) | probably_damaging(0.986) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
PMVK | SNV | Missense_Mutation | rs149231731 | c.383C>T | p.Thr128Met | p.T128M | Q15126 | protein_coding | deleterious(0.02) | probably_damaging(0.979) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PMVK | SNV | Missense_Mutation | novel | c.197G>T | p.Ser66Ile | p.S66I | Q15126 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
PMVK | SNV | Missense_Mutation | rs149231731 | c.383C>T | p.Thr128Met | p.T128M | Q15126 | protein_coding | deleterious(0.02) | probably_damaging(0.979) | TCGA-AJ-A3NE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PMVK | SNV | Missense_Mutation | c.525G>T | p.Gln175His | p.Q175H | Q15126 | protein_coding | tolerated(0.14) | benign(0) | TCGA-B5-A11E-01 | Endometrium | uterine corpus endometrioid carcinoma | 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 |
10654 | PMVK | ENZYME, KINASE | inhibitor | 135651554 |
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