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 GBA3
Basic gene info.Gene symbolGBA3
Gene nameglucosidase, beta, acid 3
SynonymsCBG|CBGL1|GLUC|KLRP
CytomapUCSC genome browser: 4p15.2
Genomic locationchr4 :22694547-22821192
Type of geneprotein-coding
RefGenesNM_001128432.2,
NM_001277225.1,NM_020973.4,NR_102355.1,NR_102356.1,
NR_102357.1,
Ensembl idENSG00000249948
Descriptioncytosolic beta-glucosidasecytosolic beta-glucosidase-like protein 1glucosidase, beta, acid 3 (cytosolic)klotho-related protein
Modification date20141211
dbXrefs MIM : 606619
HGNC : HGNC
Ensembl : ENSG00000249948
HPRD : 09428
Vega : OTTHUMG00000160448
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GBA3
BioGPS: 57733
Gene Expression Atlas: ENSG00000249948
The Human Protein Atlas: ENSG00000249948
PathwayNCI Pathway Interaction Database: GBA3
KEGG: GBA3
REACTOME: GBA3
ConsensusPathDB
Pathway Commons: GBA3
MetabolismMetaCyc: GBA3
HUMANCyc: GBA3
RegulationEnsembl's Regulation: ENSG00000249948
miRBase: chr4 :22,694,547-22,821,192
TargetScan: NM_001128432
cisRED: ENSG00000249948
ContextiHOP: GBA3
cancer metabolism search in PubMed: GBA3
UCL Cancer Institute: GBA3
Assigned class in ccmGDBC

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Phenotypic Information for GBA3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GBA3
Familial Cancer Database: GBA3
* 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_GLYCOSPHINGOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GBA3
MedGen: GBA3 (Human Medical Genetics with Condition)
ClinVar: GBA3
PhenotypeMGI: GBA3 (International Mouse Phenotyping Consortium)
PhenomicDB: GBA3

Mutations for GBA3
* 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
ovaryGBA3chr42278895522788975GBA3chr42278297222782992
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 GBA3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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        1      
GAIN (# sample) 1        1      
LOSS (# sample)                 
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=60)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr4:22749269-22749269p.R213*4
chr4:22749486-22749486p.R285T2
chr4:22820448-22820448p.V438I2
chr4:22749597-22749597p.G322E2
chr4:22820418-22820418p.G428R2
chr4:22749243-22749243p.S204C2
chr4:22748966-22748966p.V112F1
chr4:22749320-22749320p.E230K1
chr4:22750561-22750561p.Q395Q1
chr4:22820428-22820428p.S431I1

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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=0

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                    
# mutation                    
nonsynonymous SNV                    
synonymous SNV                    
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

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 GBA3 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 GBA3

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

ADAM18,BAGE,C11orf53,NAT16,CLCA1,CT47A11,DDC,
FLJ25363,GBA3,HAND1,HTR2C,KCNA4,KCNK12,KRTAP9-4,
KRTAP9-9,LOC360030,POU4F2,RLN3,SEC14L3,SHH,SPANXA2
CDKN2AIP,GBA3,GUCA1C,KANSL1,KRTAP12-2,CERS3,MAP3K1,
MMS19,STK26,NKX6-2,OR4A47,OR52B2,OR6S1,OVCH2,
PARP16,PTPRZ1,SCN2A,SNHG1,TMCO6,WIF1,ZNF354A

AMPD1,ADTRP,CA2,CASR,CDKN2B-AS1,CYP2C18,DRD5,
DUSP21,ENPP6,GBA3,GPT,GUCA2B,HSD3B2,MEP1B,
MS4A12,NR1H4,OTOP2,SLC17A8,SLC25A34,SLC30A10,TMIGD1
ACE2,ANPEP,ADIRF,CHN2,FLVCR1,G6PC,GBA3,
SLC52A1,HEBP1,MEP1B,MS4A8,NAT8B,OTC,PCK2,
PEPD,PKLR,PTGR1,SLC17A8,SLC23A1,SLC6A4,AGMO
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 GBA3


There's no related Drug.
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Cross referenced IDs for GBA3
* 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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