Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for GLYCTK
Basic gene info.Gene symbolGLYCTK
Gene nameglycerate kinase
SynonymsHBEBP2|HBEBP4|HBeAgBP4A
CytomapUCSC genome browser: 3p21.1
Genomic locationchr3 :52321835-52327021
Type of geneprotein-coding
RefGenesNM_001144951.1,
NM_145262.3,NR_026699.1,NR_026700.1,NR_026701.1,
NR_026702.1,
Ensembl idENSG00000168237
DescriptionHBeAg binding protein 4HBeAg-binding protein 2
Modification date20141207
dbXrefs MIM : 610516
HGNC : HGNC
Ensembl : ENSG00000168237
HPRD : 13586
Vega : OTTHUMG00000158380
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GLYCTK
BioGPS: 132158
Gene Expression Atlas: ENSG00000168237
The Human Protein Atlas: ENSG00000168237
PathwayNCI Pathway Interaction Database: GLYCTK
KEGG: GLYCTK
REACTOME: GLYCTK
ConsensusPathDB
Pathway Commons: GLYCTK
MetabolismMetaCyc: GLYCTK
HUMANCyc: GLYCTK
RegulationEnsembl's Regulation: ENSG00000168237
miRBase: chr3 :52,321,835-52,327,021
TargetScan: NM_001144951
cisRED: ENSG00000168237
ContextiHOP: GLYCTK
cancer metabolism search in PubMed: GLYCTK
UCL Cancer Institute: GLYCTK
Assigned class in ccmGDBC

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Phenotypic Information for GLYCTK(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GLYCTK
Familial Cancer Database: GLYCTK
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

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/

check002.gifMetabolic Pathway Description
KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM
KEGG_GLYCEROLIPID_METABOLISM
KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GLYCTK
MedGen: GLYCTK (Human Medical Genetics with Condition)
ClinVar: GLYCTK
PhenotypeMGI: GLYCTK (International Mouse Phenotyping Consortium)
PhenomicDB: GLYCTK

Mutations for GLYCTK
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GLYCTK related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU752122GLYCTK179235232741252327487PSG388148194326218443262244

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr3:52326621-52326621p.L351V2
chr3:52326290-52326290p.I240I2
chr3:52325015-52325015p.F139F2
chr3:52326932-52326932p.Q454H2
chr3:52324415-52324415p.L19L2
chr3:52325039-52325039p.P147P2
chr3:52324538-52324538p.S60S2
chr3:52325777-52325777p.L182V1
chr3:52326611-52326611p.F347L1
chr3:52324696-52324696p.P113L1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample32 2  1 1  4    8515
# mutation32 2  1 1  4    7515
nonsynonymous SNV32 2  1 1  2    13 2
synonymous SNV           2    6213
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr3:52324415p.L19L,GLYCTK2
chr3:52324538p.S60S,GLYCTK2
chr3:52325015p.F139F,GLYCTK2
chr3:52326603p.L182V1
chr3:52325046p.V512V1
chr3:52326740p.R205C1
chr3:52325055p.L518F1
chr3:52326768p.R205L1
chr3:52325072p.P182L1
chr3:52326770p.R184K,GLYCTK1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for GLYCTK 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 GLYCTK

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-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

: Open all plots for all cancer types

C16orf86,TMEM259,C21orf2,CAMK1,CAPN10,CCDC88B,EXOC3L1,
FBXL15,GLYCTK,GRASP,IFFO1,KANK3,LYL1,MBD3,
NDUFS7,PPP1R12C,SCRN2,SELO,SNRNP70,TNFRSF14,USHBP1
ACSM2A,ACSM2B,AMN,APOC3,APOL4,ASS1,BMP3,
TBATA,IZUMO4,CALCRL,GLUL,GLYCTK,LOC100101938,MOGAT1,
NDRG4,NTSR2,PDZD7,PMM1,RASL10B,SNORA14A,ST8SIA3

ABCC6P1,ACOT11,ACY1,SMIM24,RBBP8NL,CYB561D2,CYP2D6,
DAK,DDC,GLYCTK,HDHD3,HEMK1,IFRD2,METTL7B,
MYO1A,OGFOD2,SLC51B,PMM2,SLC39A5,TUBAL3,TUSC2
ACY1,AKR7A3,AKR7L,SOWAHA,CDHR5,CYP2B6,CYP2C18,
CYP4F12,DAPK2,GDA,SLX1B,GLYCTK,INPP5J,MYO1A,
PCK2,PDXP,PRAP1,RBKS,SLC23A3,SLC39A5,TMEM120A
check002.gifCo-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

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for GLYCTK


There's no related Drug.
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Cross referenced IDs for GLYCTK
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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