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 GYG2
Basic gene info.Gene symbolGYG2
Gene nameglycogenin 2
SynonymsGN-2|GN2
CytomapUCSC genome browser: Xp22.3
Genomic locationchrX :2746862-2800861
Type of geneprotein-coding
RefGenesNM_001079855.1,
NM_001184702.1,NM_001184703.1,NM_001184704.1,NM_003918.2,
Ensembl idENSG00000056998
Descriptionglycogenin glucosyltransferaseglycogenin-2
Modification date20141207
dbXrefs MIM : 300198
HGNC : HGNC
Ensembl : ENSG00000056998
HPRD : 02185
Vega : OTTHUMG00000021079
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GYG2
BioGPS: 8908
Gene Expression Atlas: ENSG00000056998
The Human Protein Atlas: ENSG00000056998
PathwayNCI Pathway Interaction Database: GYG2
KEGG: GYG2
REACTOME: GYG2
ConsensusPathDB
Pathway Commons: GYG2
MetabolismMetaCyc: GYG2
HUMANCyc: GYG2
RegulationEnsembl's Regulation: ENSG00000056998
miRBase: chrX :2,746,862-2,800,861
TargetScan: NM_001079855
cisRED: ENSG00000056998
ContextiHOP: GYG2
cancer metabolism search in PubMed: GYG2
UCL Cancer Institute: GYG2
Assigned class in ccmGDBC

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Phenotypic Information for GYG2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GYG2
Familial Cancer Database: GYG2
* 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
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GYG2
MedGen: GYG2 (Human Medical Genetics with Condition)
ClinVar: GYG2
PhenotypeMGI: GYG2 (International Mouse Phenotyping Consortium)
PhenomicDB: GYG2

Mutations for GYG2
* 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 GYG2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF309900GYG2275X27613512772049GYG266678X27721292779598
U94359EMB1264654969386149707829GYG226404066X27987412800155

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=36)
Stat. for Synonymous SNVs
(# total SNVs=13)
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
chr23:2795286-2795286p.E428K3
chr23:2761348-2761348p.T65T2
chr23:2773087-2773087p.P157P2
chr23:2761050-2761050p.H7Y2
chr23:2778030-2778030p.T285M2
chr23:2795308-2795308p.A435D2
chr23:2772118-2772118p.G114R2
chr23:2773196-2773196p.G194R1
chr23:2778088-2778088p.R304R1
chr23:2795326-2795326p.P441L1

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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
# sample 3 72 1  1 241  22 5
# mutation 3 82 1  1 241  22 5
nonsynonymous SNV 2 5  1  1 231  12 4
synonymous SNV 1 32       1   1  1
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
chrX:2772118p.T34T,GYG22
chrX:2761348p.G83R,GYG22
chrX:2779761p.F48L,GYG21
chrX:2772069p.I52N,GYG21
chrX:2773196p.G62R,GYG21
chrX:2795258p.I66I,GYG21
chrX:2772079p.G62E,GYG21
chrX:2774565p.D70N,GYG21
chrX:2795308p.S77L,GYG21
chrX:2772094p.A75T,GYG21

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 GYG2 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 GYG2

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

ACVR1C,ADH1A,ADH1B,ADIPOQ,AOC3,AQP7,AQPEP,
C14orf180,CIDEC,GLYAT,GPD1,GYG2,HEPACAM,HEPN1,
KCNIP2,KLB,LIPE,PLIN1,PLIN4,SLC19A3,TMEM132C
ABHD15,ACO1,FAM213A,CIDEC,ESYT1,FAM89A,FBXO27,
GNAI1,GYG2,HEPACAM,HRASLS5,KCNIP2,LPL,MARC1,
PDE3B,PECR,PEX19,PLIN1,PPARG,SIK2,TYRO3

ARSE,CTPS2,EIF1AX,FARP1,FUNDC1,GEMIN8,GYG2,
HDHD1,KDM5C,NAALADL2,OFD1,JADE3,RNF43,SCML1,
SHROOM4,SYAP1,TAB3,TXLNG,XIST,ZBED1,ZRSR2
CDC25B,CHI3L1,CLEC4GP1,CPXM1,CST11,DPPA3,DPYS,
GYG2,LOC55908,LOC728723,LPL,MARCO,NKX6-2,PCSK9,
PLTP,REG1A,REG1B,RNASE2,SCD,SLC7A10,THRSP
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 GYG2


There's no related Drug.
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Cross referenced IDs for GYG2
* 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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