Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	GNB3
	Gene name	guanine nucleotide binding protein (G protein), beta polypeptide 3
	Synonyms	-
	Cytomap	UCSC genome browser: 12p13
	Genomic location	chr12 :6949374-6956557
	Type of gene	protein-coding
	RefGenes	NM_001297571.1, NM_002075.3,
	Ensembl id	ENSG00000268195
	Description	G 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 date	20141207
dbXrefs	MIM : 139130
	HGNC : HGNC
	Ensembl : ENSG00000111664
	HPRD : 00743
	Vega : OTTHUMG00000168517
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GNB3
	BioGPS: 2784
	Gene Expression Atlas: ENSG00000268195
	The Human Protein Atlas: ENSG00000268195
Pathway	NCI Pathway Interaction Database: GNB3
	KEGG: GNB3
	REACTOME: GNB3
	ConsensusPathDB
	Pathway Commons: GNB3
Metabolism	MetaCyc: GNB3
	HUMANCyc: GNB3
Regulation	Ensembl's Regulation: ENSG00000268195
	miRBase: chr12 :6,949,374-6,956,557
	TargetScan: NM_001297571
	cisRED: ENSG00000268195
Context	iHOP: GNB3
	cancer metabolism search in PubMed: GNB3
	UCL Cancer Institute: GNB3
Assigned class in ccmGDB	C

Top

Phenotypic Information for GNB3(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: GNB3
	MedGen: GNB3 (Human Medical Genetics with Condition)
	ClinVar: GNB3
Phenotype	MGI: GNB3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GNB3 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BM715141	INTS9	1	300	8	28654229	28654528	GNB3	286	353	12	6956490	6956557
BM691769	INTS9	1	300	8	28654229	28654528	GNB3	286	353	12	6956490	6956557
BU734248	GNB3	18	304	12	6956276	6956557	GNB3	286	351	12	6956204	6956269
BM665849	GNB3	18	85	12	6956490	6956557	INTS9	71	366	8	28654233	28654528

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

Top

SNV 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

Top

Somatic 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.

Top

Top 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 position	Mutation(aa)	Unique sampleID count
chr12:6954875-6954875	p.S275S	2
chr12:6953134-6953134	p.A231T	2
chr12:6952161-6952161	p.R42*	2
chr12:6952642-6952642	p.S128F	1
chr12:6955968-6955968	p.G310A	1
chr12:6953089-6953089	p.G216R	1
chr12:6952169-6952169	p.Q44Q	1
chr12:6954864-6954864	p.G272S	1
chr12:6952647-6952647	p.E130*	1
chr12:6956008-6956008	p.D323D	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	2	1	7			2		1			5	3			1	6	3		5
# mutation	2	2	1	7			2		1			6	3			1	7	3		5
nonsynonymous SNV	2	2	1	4			2					5	1			1	7	1		3
synonymous SNV				3					1			1	2					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])

Top

Top 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 Position	Mutation(aa)	Unique sampleID count
chr12:6952957	p.F111V,GNB3	1
chr12:6954785	p.I231I,GNB3	1
chr12:6952186	p.G115W,GNB3	1
chr12:6952968	p.P235P,GNB3	1
chr12:6954793	p.I123V,GNB3	1
chr12:6952194	p.S244S,GNB3	1
chr12:6952995	p.S128F,GNB3	1
chr12:6954826	p.A247D,GNB3	1
chr12:6952582	p.R129H,GNB3	1
chr12:6953059	p.Q258R,GNB3	1

Other 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

Copy 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]

Top

Gene Expression for GNB3

Gene 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.

Differential 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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

Gene-Gene Network Information

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for GNB3

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00575	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Clonidine
DB00363	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Clozapine
DB00540	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Nortriptyline
DB00918	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved; investigational	Almotriptan
DB00334	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved; investigational	Olanzapine
DB00216	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved; investigational	Eletriptan
DB00952	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved; investigational	Naratriptan
DB00953	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Rizatriptan
DB00669	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved; investigational	Sumatriptan
DB00315	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved; investigational	Zolmitriptan
DB00203	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved; investigational	Sildenafil
DB01076	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Atorvastatin
DB01095	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Fluvastatin
DB00227	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved; investigational	Lovastatin
DB00175	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Pravastatin
DB01098	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Rosuvastatin
DB00641	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Simvastatin
DB00177	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved; investigational	Valsartan
DB01392	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Yohimbine
DB01105	guanine nucleotide binding protein (G protein), beta polypeptide 3	illicit; approved; withdrawn; investigational	Sibutramine
DB00999	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Hydrochlorothiazide
DB00335	guanine nucleotide binding protein (G protein), beta polypeptide 3	approved	Atenolol

Top

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