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 GBE1
Basic gene info.Gene symbolGBE1
Gene nameglucan (1,4-alpha-), branching enzyme 1
SynonymsAPBD|GBE|GSD4
CytomapUCSC genome browser: 3p12.3
Genomic locationchr3 :81538849-81810950
Type of geneprotein-coding
RefGenesNM_000158.3,
Ensembl idENSG00000114480
Description1,4-alpha-glucan-branching enzymeamylo-(1,4 to 1,6) transglucosidaseamylo-(1,4 to 1,6) transglycosylasebrancher enzymeglycogen branching enzymeglycogen-branching enzyme
Modification date20141219
dbXrefs MIM : 607839
HGNC : HGNC
Ensembl : ENSG00000114480
HPRD : 01985
Vega : OTTHUMG00000158978
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GBE1
BioGPS: 2632
Gene Expression Atlas: ENSG00000114480
The Human Protein Atlas: ENSG00000114480
PathwayNCI Pathway Interaction Database: GBE1
KEGG: GBE1
REACTOME: GBE1
ConsensusPathDB
Pathway Commons: GBE1
MetabolismMetaCyc: GBE1
HUMANCyc: GBE1
RegulationEnsembl's Regulation: ENSG00000114480
miRBase: chr3 :81,538,849-81,810,950
TargetScan: NM_000158
cisRED: ENSG00000114480
ContextiHOP: GBE1
cancer metabolism search in PubMed: GBE1
UCL Cancer Institute: GBE1
Assigned class in ccmGDBC

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Phenotypic Information for GBE1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GBE1
Familial Cancer Database: GBE1
* 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_STARCH_AND_SUCROSE_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GBE1
MedGen: GBE1 (Human Medical Genetics with Condition)
ClinVar: GBE1
PhenotypeMGI: GBE1 (International Mouse Phenotyping Consortium)
PhenomicDB: GBE1

Mutations for GBE1
* 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
pancreasGBE1chr38176443981764459GBE1chr38171160981711629
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 GBE1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF346361PLCB45826212091495719149611GBE162164838178015681780186
CA428629GBE1212038156261681562736ITGA3118556174814561748149439

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 # sample111       2  2   
GAIN (# sample)1         1  2   
LOSS (# sample) 11       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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=52)
Stat. for Synonymous SNVs
(# total SNVs=20)
Stat. for Deletions
(# total SNVs=2)
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
chr3:81754677-81754677p.G77G3
chr3:81643118-81643118p.R350H3
chr3:81754702-81754702p.F69C2
chr3:81640303-81640303p.S374*2
chr3:81699052-81699052p.S150S2
chr3:81695576-81695576p.G250A2
chr3:81586104-81586104p.M587I2
chr3:81691953-81691953p.S324N1
chr3:81754676-81754676p.V78I1
chr3:81586172-81586172p.R565W1

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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
# sample24 13    1  222 194113
# mutation14 12    1  222 194114
nonsynonymous SNV13 9    1  22  194 10
synonymous SNV 1 3         2    14
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
chr3:81643118p.T402T2
chr3:81586104p.M587I2
chr3:81699052p.S150S2
chr3:81640218p.R350H2
chr3:81720086p.R166C1
chr3:81630325p.F616S1
chr3:81640303p.G382G1
chr3:81698054p.R156C1
chr3:81548282p.N611D1
chr3:81754616p.S378N1

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 GBE1 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 GBE1

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

ANO6,ATP6V1A,EOGT,CCNYL1,CD109,CHMP2B,CSGALNACT2,
ERO1L,FERMT2,FNDC3B,FUT11,GBE1,ITGAV,ITGB1,
KIAA1715,LIMS1,LOX,NCKAP1,P4HA1,PTPLB,ZNF654
ACAA2,ACO1,ACSS2,BNIP3,PQLC2L,CIDEC,FAM89A,
GBE1,GYG2,HSDL2,MARC1,MTHFD1,PEX19,PFKFB1,
PPARG,PPP1R1A,PRDX6,PRKAR2B,RNF157,STBD1,TSPAN3

BNIP3L,TMEM263,C4orf3,CA9,ERO1L,FUT11,GBE1,
HIF1A,LDHA,MAPK6,P4HA1,PDK1,PFKFB3,PGAM1,
PLOD2,SEC24D,SSR3,STC1,TMEM45A,TMTC3,ZNF654
ANXA2P1,CAND1,DLD,EPB41L2,FBXL17,GBE1,HNRNPK,
HSPA4,IDE,INTS4P1,KIAA1279,NARS,PAK2,PARG,
PPP3R1,PSMD1,RAB14,RDH8,UBE3A,UBP1,YME1L1
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 GBE1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01033glucan (1,4-alpha-), branching enzyme 1approvedMercaptopurine
DB00563glucan (1,4-alpha-), branching enzyme 1approvedMethotrexate


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Cross referenced IDs for GBE1
* 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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