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 GNB3
Basic gene info.Gene symbolGNB3
Gene nameguanine nucleotide binding protein (G protein), beta polypeptide 3
Synonyms-
CytomapUCSC genome browser: 12p13
Genomic locationchr12 :6949374-6956557
Type of geneprotein-coding
RefGenesNM_001297571.1,
NM_002075.3,
Ensembl idENSG00000268195
DescriptionG protein, beta-3 subunitGTP-binding regulatory protein beta-3 chainguanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 3guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-3hypertension associated proteintransducin beta chain 3
Modification date20141207
dbXrefs MIM : 139130
HGNC : HGNC
Ensembl : ENSG00000111664
HPRD : 00743
Vega : OTTHUMG00000168517
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNB3
BioGPS: 2784
Gene Expression Atlas: ENSG00000268195
The Human Protein Atlas: ENSG00000268195
PathwayNCI Pathway Interaction Database: GNB3
KEGG: GNB3
REACTOME: GNB3
ConsensusPathDB
Pathway Commons: GNB3
MetabolismMetaCyc: GNB3
HUMANCyc: GNB3
RegulationEnsembl's Regulation: ENSG00000268195
miRBase: chr12 :6,949,374-6,956,557
TargetScan: NM_001297571
cisRED: ENSG00000268195
ContextiHOP: GNB3
cancer metabolism search in PubMed: GNB3
UCL Cancer Institute: GNB3
Assigned class in ccmGDBC

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Phenotypic Information for GNB3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GNB3
Familial Cancer Database: GNB3
* 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_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: GNB3
MedGen: GNB3 (Human Medical Genetics with Condition)
ClinVar: GNB3
PhenotypeMGI: GNB3 (International Mouse Phenotyping Consortium)
PhenomicDB: GNB3

Mutations for GNB3
* 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 GNB3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM715141INTS9130082865422928654528GNB32863531269564906956557
BM691769INTS9130082865422928654528GNB32863531269564906956557
BU734248GNB3183041269562766956557GNB32863511269562046956269
BM665849GNB318851269564906956557INTS97136682865423328654528

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=24)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr12:6954875-6954875p.S275S2
chr12:6953134-6953134p.A231T2
chr12:6952161-6952161p.R42*2
chr12:6952186-6952186p.T50M1
chr12:6954874-6954874p.S275C1
chr12:6952794-6952794p.?1
chr12:6950463-6950463p.M4I1
chr12:6953130-6953130p.I229M1
chr12:6952194-6952194p.G53R1
chr12:6952822-6952822p.D153Y1

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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
# sample2217  2 1  53  163 5
# mutation2217  2 1  63  173 5
nonsynonymous SNV2214  2    51  171 3
synonymous SNV   3    1  12    2 2
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
chr12:6952582p.M4I,GNB31
chr12:6953059p.L139F,GNB31
chr12:6950463p.E259K,GNB31
chr12:6954828p.E5E,GNB31
chr12:6952590p.C148F,GNB31
chr12:6953077p.S264F,GNB31
chr12:6950466p.D20G,GNB31
chr12:6954844p.E171K,GNB31
chr12:6952602p.E266K,GNB31
chr12:6953089p.A24P,GNB31

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 GNB3 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 GNB3

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

AGER,ATAD3A,ATAD3B,CDK3,CENPT,DDX12P,FAM156A,
GNB3,KCNAB3,KLHL17,LEPREL2,LOC642846,LY6G5B,MEF2B,
NT5DC2,PIF1,SCX,TAF1C,TOP3B,TRABD,ZDHHC8
AMT,ANKZF1,APBB3,ATG16L2,CCNL2,CENPT,DCST2,
FAM193B,GNB3,HSF4,KAT2A,LUC7L,NEIL1,NSUN5P1,
NSUN5P2,PABPC1L,SLC23A3,SNHG10,SNHG12,ZGLP1,ZNF692

LINC00341,C9orf139,CALHM1,CBLN3,CELF6,CHKB-CPT1B,DPY19L2,
GNB3,HHIPL2,KCNAB3,KIAA0125,LEPREL2,LOC100128288,MIAT,
NEURL4,PLCB2,PVRIG,RASSF1,SGSM2,UCP3,VAMP1
CSF2RB,E2F3,EYA3,FCRL5,GLCCI1,GNB3,ITGA8,
KCNA3,KLHL6,LAX1,NUP210,OSBPL3,PDE7A,PIK3CG,
PIM2,PLCG2,POU2AF1,PRDM15,SEMA4A,SFMBT2,SYVN1
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 GNB3
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
DB00575guanine nucleotide binding protein (G protein), beta polypeptide 3approvedClonidine
DB00363guanine nucleotide binding protein (G protein), beta polypeptide 3approvedClozapine
DB00540guanine nucleotide binding protein (G protein), beta polypeptide 3approvedNortriptyline
DB00918guanine nucleotide binding protein (G protein), beta polypeptide 3approved; investigationalAlmotriptan
DB00334guanine nucleotide binding protein (G protein), beta polypeptide 3approved; investigationalOlanzapine
DB00216guanine nucleotide binding protein (G protein), beta polypeptide 3approved; investigationalEletriptan
DB00952guanine nucleotide binding protein (G protein), beta polypeptide 3approved; investigationalNaratriptan
DB00953guanine nucleotide binding protein (G protein), beta polypeptide 3approvedRizatriptan
DB00669guanine nucleotide binding protein (G protein), beta polypeptide 3approved; investigationalSumatriptan
DB00315guanine nucleotide binding protein (G protein), beta polypeptide 3approved; investigationalZolmitriptan
DB00203guanine nucleotide binding protein (G protein), beta polypeptide 3approved; investigationalSildenafil
DB01076guanine nucleotide binding protein (G protein), beta polypeptide 3approvedAtorvastatin
DB01095guanine nucleotide binding protein (G protein), beta polypeptide 3approvedFluvastatin
DB00227guanine nucleotide binding protein (G protein), beta polypeptide 3approved; investigationalLovastatin
DB00175guanine nucleotide binding protein (G protein), beta polypeptide 3approvedPravastatin
DB01098guanine nucleotide binding protein (G protein), beta polypeptide 3approvedRosuvastatin
DB00641guanine nucleotide binding protein (G protein), beta polypeptide 3approvedSimvastatin
DB00177guanine nucleotide binding protein (G protein), beta polypeptide 3approved; investigationalValsartan
DB01392guanine nucleotide binding protein (G protein), beta polypeptide 3approvedYohimbine
DB01105guanine nucleotide binding protein (G protein), beta polypeptide 3illicit; approved; withdrawn; investigationalSibutramine
DB00999guanine nucleotide binding protein (G protein), beta polypeptide 3approvedHydrochlorothiazide
DB00335guanine nucleotide binding protein (G protein), beta polypeptide 3approvedAtenolol


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Cross referenced IDs for GNB3
* 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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