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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GK |
Basic gene info. | Gene symbol | GK |
Gene name | glycerol kinase | |
Synonyms | GK1|GKD | |
Cytomap | UCSC genome browser: Xp21.3 | |
Genomic location | chrX :30671475-30749577 | |
Type of gene | protein-coding | |
RefGenes | NM_000167.5, NM_001128127.2,NM_001205019.1,NM_203391.3, | |
Ensembl id | ENSG00000198814 | |
Description | ATP:glycerol 3-phosphotransferaseglycerokinase | |
Modification date | 20141207 | |
dbXrefs | MIM : 300474 | |
HGNC : HGNC | ||
Ensembl : ENSG00000198814 | ||
HPRD : 08363 | ||
Vega : OTTHUMG00000021328 | ||
Protein | UniProt: P32189 go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GK | |
BioGPS: 2710 | ||
Gene Expression Atlas: ENSG00000198814 | ||
The Human Protein Atlas: ENSG00000198814 | ||
Pathway | NCI Pathway Interaction Database: GK | |
KEGG: GK | ||
REACTOME: GK | ||
ConsensusPathDB | ||
Pathway Commons: GK | ||
Metabolism | MetaCyc: GK | |
HUMANCyc: GK | ||
Regulation | Ensembl's Regulation: ENSG00000198814 | |
miRBase: chrX :30,671,475-30,749,577 | ||
TargetScan: NM_000167 | ||
cisRED: ENSG00000198814 | ||
Context | iHOP: GK | |
cancer metabolism search in PubMed: GK | ||
UCL Cancer Institute: GK | ||
Assigned class in ccmGDB | A - This gene has a literature evidence and it belongs to cancer gene. | |
References showing role of GK in cancer cell metabolism | 1. Szlyk B, Braun CR, Ljubicic S, Patton E, Bird GH, et al. (2014) A phospho-BAD BH3 helix activates glucokinase by a mechanism distinct from that of allosteric activators. Nat Struct Mol Biol 21: 36-42. doi: 10.1038/nsmb.2717. pmid: 4084830. go to article 2. Dong H, Yang X, Xie J, Xiang L, Li Y, et al. (2015) UP12, a novel ursolic acid derivative with potential for targeting multiple signaling pathways in hepatocellular carcinoma. Biochem Pharmacol 93: 151-162. doi: 10.1016/j.bcp.2014.11.014. go to article |
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Phenotypic Information for GK(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GK |
Familial Cancer Database: GK |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
Metabolic Pathway Description | |
KEGG_GLYCEROLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS |
Others | |
OMIM | 300474; gene. 307030; phenotype. |
Orphanet | 284408; Glycerol kinase deficiency, infantile form. 284411; Glycerol kinase deficiency, juvenile form. 284414; Glycerol kinase deficiency, adult form. |
Disease | KEGG Disease: GK |
MedGen: GK (Human Medical Genetics with Condition) | |
ClinVar: GK | |
Phenotype | MGI: GK (International Mouse Phenotyping Consortium) |
PhenomicDB: GK |
Mutations for GK |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GK related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
AA089671 | TPM1 | 1 | 138 | 15 | 63351810 | 63353135 | GK | 125 | 145 | X | 30686569 | 30686589 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=3) | (# total SNVs=1) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 10 SNVs Having the Most Samples in COSMIC data |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr23:30738181-30738181 | p.A402V | 1 |
chr23:30739085-30739085 | p.R492W | 1 |
chr23:30671719-30671719 | p.S22L | 1 |
chr23:30712588-30712588 | p.R162R | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample |   | 1 | 1 | 7 |   |   | 1 |   | 1 |   |   | 6 | 3 |   |   | 1 | 5 | 2 |   | 16 |
# mutation |   | 1 | 1 | 6 |   |   | 1 |   | 1 |   |   | 7 | 3 |   |   | 1 | 4 | 2 |   | 21 |
nonsynonymous SNV |   | 1 |   | 5 |   |   | 1 |   | 1 |   |   | 6 | 3 |   |   | 1 | 4 | 2 |   | 16 |
synonymous SNV |   |   | 1 | 1 |   |   |   |   |   |   |   | 1 |   |   |   |   |   |   |   | 5 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
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Top 10 SNVs Having the Most Samples in TCGA data |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chrX:30671719 | p.S22L,GK | 3 |
chrX:30736685 | p.R330C,GK | 2 |
chrX:30712558 | p.S212Y,GK | 1 |
chrX:30742280 | p.D414Y,GK | 1 |
chrX:30719001 | p.S22S,GK | 1 |
chrX:30671720 | p.D216D,GK | 1 |
chrX:30738765 | p.G416R,GK | 1 |
chrX:30712588 | p.T32A,GK | 1 |
chrX:30742289 | p.C220C,GK | 1 |
chrX:30719011 | p.L434I,GK | 1 |
Other DBs for Point Mutations |
Copy Number for GK in TCGA |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
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Gene Expression for GK |
Gene Expression in Cancer Cell-lines (CCLE) |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
Differential Gene Expression in Primary Tumors (TCGA) |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-Expressed gene's network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
ACTR3BP2,GK2,KRTAP19-2,KRTAP25-1,KRTAP6-1,OR10H3,OR4C16, OR4L1,OR51A4,OR51G1,OR52A5,OR52J3,OR5D18,OR5I1, OR5L1,OR5L2,OR6C65,OR6C75,OR8H3,POM121L12,REG1P | ALB,ANGPTL3,BCO1,HNF1A-AS1,LINC00470___CHMP1B,DPY19L2,GK2, GNAT3,LOC153328,MAGEB2,MIA2,MTNR1B,OR5D16,PKHD1, POTEC,POTED,SCARNA15,SNORA71A,TAAR9,UGT2B15,UTS2 |
ADAD2,BRDT,CT47A2,CT47A6,DCAF8L2,DUPD1,FAM9B, GAGE2C,GK2,LOC100287704,NF1P1,NOBOX,OR51B6,OR51F2, OR52A5,OR52E6,OR9I1,POM121L12,TNNI3K,TNP1,TUBA3C | NA,NA,NA,NA,NA,NA,NA, NA,NA,NA,NA,NA,NA,NA, NA,NA,NA,NA,NA,NA,NA |
Co-Expressed gene's Protein-protein interaction Network Plot |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for GK |
There's no related Drug. |
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Cross referenced IDs for GK |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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