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 GYG1
Basic gene info.Gene symbolGYG1
Gene nameglycogenin 1
SynonymsGSD15|GYG
CytomapUCSC genome browser: 3q24-q25.1
Genomic locationchr3 :148709194-148745456
Type of geneprotein-coding
RefGenesNM_001184720.1,
NM_001184721.1,NM_004130.3,
Ensembl idENSG00000163754
DescriptionGN-1glycogenin glucosyltransferaseglycogenin-1
Modification date20141207
dbXrefs MIM : 603942
HGNC : HGNC
Ensembl : ENSG00000163754
HPRD : 06805
Vega : OTTHUMG00000159533
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GYG1
BioGPS: 2992
Gene Expression Atlas: ENSG00000163754
The Human Protein Atlas: ENSG00000163754
PathwayNCI Pathway Interaction Database: GYG1
KEGG: GYG1
REACTOME: GYG1
ConsensusPathDB
Pathway Commons: GYG1
MetabolismMetaCyc: GYG1
HUMANCyc: GYG1
RegulationEnsembl's Regulation: ENSG00000163754
miRBase: chr3 :148,709,194-148,745,456
TargetScan: NM_001184720
cisRED: ENSG00000163754
ContextiHOP: GYG1
cancer metabolism search in PubMed: GYG1
UCL Cancer Institute: GYG1
Assigned class in ccmGDBC

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Phenotypic Information for GYG1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GYG1
Familial Cancer Database: GYG1
* 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: GYG1
MedGen: GYG1 (Human Medical Genetics with Condition)
ClinVar: GYG1
PhenotypeMGI: GYG1 (International Mouse Phenotyping Consortium)
PhenomicDB: GYG1

Mutations for GYG1
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasGYG1chr3148718014148718034GYG1chr3148735959148735979
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GYG1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB445243BIRC616218123267690332676922GYG11744333148714087148714611
BU677172GYG1182453148745192148745419GYG12413973148745039148745195

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample 1 2  1   1      
GAIN (# sample) 1 2      1      
LOSS (# sample)      1          
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=17)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=5)
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
chr3:148744643-148744645p.E326delE4
chr3:148727126-148727126p.H182P2
chr3:148727133-148727133p.P184P2
chr3:148714590-148714590p.G127A1
chr3:148741967-148741967p.L246I1
chr3:148714147-148714147p.D68N1
chr3:148744703-148744703p.D346N1
chr3:148714596-148714596p.P129L1
chr3:148741973-148741973p.L248M1
chr3:148714159-148714159p.L72V1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 2 2  2    113  16 4
# mutation 2 2  2    113  16 4
nonsynonymous SNV 2 1  2    113  14 3
synonymous SNV   1             2 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
chr3:148714574p.R180I,GYG11
chr3:148744285p.P199Q,GYG11
chr3:148714590p.N239N,GYG11
chr3:148744621p.L248M,GYG11
chr3:148714612p.L35P,GYG11
chr3:148744654p.V37M,GYG11
chr3:148712025p.V274I,GYG11
chr3:148714687p.D68N,GYG11
chr3:148744693p.D279E1
chr3:148712030p.L72V,GYG11

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 GYG1 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 GYG1

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

ATG3,COMMD2,COPB2,DHX36,GDI2,GMPS,GYG1,
HPS3,KPNA4,MDH1,MFSD1,MRPL3,MRPS22,NAA50,
NCK1,PDCD10,RPN1,SEC61A1,SRPRB,SSR3,TFG
ATP2B2,CAND2,MCU,YBX3,FHL3,FNDC5,GYG1,
HHATL,IDI2,MAMSTR,NPY6R,OTUD1,PDLIM3,PEBP4,
PPP1R3C,SH3BGR,SMTNL2,TPM3,TRIM7,VDAC3,MSS51

ACTL6A,C6orf57,CAPZA2,COMMD10,COMMD2,CRBN,DNAJC19,
DPH3,GYG1,MED28,MYNN,NDUFB4,NDUFB5,NIT2,
PCNP,PDCD10,RNF13,RYK,SELT,SNX3,STARD3NL
ANGPTL1,PIFO,CFL2,DSTN,GYG1,HSPB8,ILK,
KCNJ8,LGALS1,LOC728819,MORN5,NECAB1,PSD,RAB34,
RASSF8,REEP1,SELM,SH3BGRL,TMEM35,TMEM55A,TSPAN2
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 GYG1


There's no related Drug.
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Cross referenced IDs for GYG1
* 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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