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 GNB4
Basic gene info.Gene symbolGNB4
Gene nameguanine nucleotide binding protein (G protein), beta polypeptide 4
SynonymsCMTD1F
CytomapUCSC genome browser: 3q26.33
Genomic locationchr3 :179113875-179169371
Type of geneprotein-coding
RefGenesNM_021629.3,
Ensembl idENSG00000114450
DescriptionG protein beta-4 subunitguanine nucleotide-binding protein subunit beta-4transducin beta chain 4
Modification date20141207
dbXrefs MIM : 610863
HGNC : HGNC
HPRD : 09973
ProteinUniProt: Q9HAV0
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNB4
BioGPS: 59345
Gene Expression Atlas: ENSG00000114450
The Human Protein Atlas: ENSG00000114450
PathwayNCI Pathway Interaction Database: GNB4
KEGG: GNB4
REACTOME: GNB4
ConsensusPathDB
Pathway Commons: GNB4
MetabolismMetaCyc: GNB4
HUMANCyc: GNB4
RegulationEnsembl's Regulation: ENSG00000114450
miRBase: chr3 :179,113,875-179,169,371
TargetScan: NM_021629
cisRED: ENSG00000114450
ContextiHOP: GNB4
cancer metabolism search in PubMed: GNB4
UCL Cancer Institute: GNB4
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GNB4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GNB4
Familial Cancer Database: GNB4
* 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 610863; gene.
615185; phenotype.
Orphanet 352670; Autosomal dominant intermediate Charcot-Marie-Tooth disease type F.
DiseaseKEGG Disease: GNB4
MedGen: GNB4 (Human Medical Genetics with Condition)
ClinVar: GNB4
PhenotypeMGI: GNB4 (International Mouse Phenotyping Consortium)
PhenomicDB: GNB4

Mutations for GNB4
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryGNB4chr3179137144179137344chr3180185698180185898
pancreasGNB4chr3179148289179148309chr195827673858276758
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 GNB4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE155686SERPINB131310186126434861264663GNB43054913179134740179134926

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 # sample212  1  1        
GAIN (# sample)212  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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)		Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr3:179132783-179132783p.P107L2
chr3:179131259-179131259p.R214R2
chr3:179123026-179123026p.D290N2
chr3:179123046-179123046p.R283H2
chr3:179131385-179131385p.E172K2
chr3:179131506-179131506p.T165I1
chr3:179132743-179132743p.I120I1
chr3:179123136-179123136p.F253C1
chr3:179137245-179137245p.R49C1
chr3:179131509-179131509p.T164I1

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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
# sample2  9  1 1  231  45 6
# mutation2  9  1 1  231  45 6
nonsynonymous SNV1  7  1 1  131  34 4
synonymous SNV1  2       1    11 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
chr3:179123026p.D290N2
chr3:179132741p.R214G1
chr3:179137253p.L51P1
chr3:179131207p.E172K1
chr3:179132743p.R49C1
chr3:179138685p.T165I1
chr3:179131212p.R46Q1
chr3:179132751p.L152S1
chr3:179138686p.L30I1
chr3:179131230p.K127K1

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 GNB4 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 GNB4

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

ACTL6A,ANKRD36BP1,B3GNT5,COA7,CEP170,CORO1C,DCUN1D1,
FNDC3B,FOXN2,GNB4,MFN1,OSBPL11,DESI2,QKI,
RAP2A,ROCK2,SYNCRIP,YEATS2,YES1,ZCCHC11,ZNF639		ARL15,CASC4,CHIC1,CTSO,DNAJC3,FAM91A1,GNB4,
HSPA13,KRAS,MAGT1,MIER1,MOB1A,PRKAA1,RP2,
SLC30A7,SOCS4,SPCS3,TGFBR1,TMED7,TMEM30A,TMTC3

C1S,CNRIP1,DSEL,ENTPD1,FBXL7,FSTL1,GNB4,
HEG1,IL1R1,MAF,MRAS,MYO5A,NRP1,PKD2,
PLEKHO2,PLXDC2,QKI,STARD8,TCF4,VIM,ZEB2		ANGPT1,AP1S2,B3GALNT1,BLVRA,FAM229B,DUSP22,EIF5A2,
FEZ1,GNB4,GUCY1B3,KIAA0895,LOC399959,LOC644538,SLC9B2,
NME4,RAB23,RAB31,IFT22,RHOQ,TCEAL7,ZNF25
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 GNB4


There's no related Drug.
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Cross referenced IDs for GNB4
* 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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