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 GNB1
Basic gene info.Gene symbolGNB1
Gene nameguanine nucleotide binding protein (G protein), beta polypeptide 1
Synonyms-
CytomapUCSC genome browser: 1p36.33
Genomic locationchr1 :1716724-1822526
Type of geneprotein-coding
RefGenesNM_001282538.1,
NM_001282539.1,NM_002074.4,
Ensembl idENSG00000078369
DescriptionG protein, beta-1 subunitbeta subunit, signal-transducing proteins GS/GIguanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1transducin beta chain 1
Modification date20141207
dbXrefs MIM : 139380
HGNC : HGNC
Ensembl : ENSG00000078369
HPRD : 00766
Vega : OTTHUMG00000000940
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNB1
BioGPS: 2782
Gene Expression Atlas: ENSG00000078369
The Human Protein Atlas: ENSG00000078369
PathwayNCI Pathway Interaction Database: GNB1
KEGG: GNB1
REACTOME: GNB1
ConsensusPathDB
Pathway Commons: GNB1
MetabolismMetaCyc: GNB1
HUMANCyc: GNB1
RegulationEnsembl's Regulation: ENSG00000078369
miRBase: chr1 :1,716,724-1,822,526
TargetScan: NM_001282538
cisRED: ENSG00000078369
ContextiHOP: GNB1
cancer metabolism search in PubMed: GNB1
UCL Cancer Institute: GNB1
Assigned class in ccmGDBC

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Phenotypic Information for GNB1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GNB1
Familial Cancer Database: GNB1
* 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: GNB1
MedGen: GNB1 (Human Medical Genetics with Condition)
ClinVar: GNB1
PhenotypeMGI: GNB1 (International Mouse Phenotyping Consortium)
PhenomicDB: GNB1

Mutations for GNB1
* 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
ovaryGNB1chr117417161741736GNB1chr117720001772020
ovaryGNB1chr117426651742685GNB1chr117442841744304
ovaryGNB1chr117862921786312GNB1chr117699061769926
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 GNB1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF974736GNB1264117173031717365GNB162127117172431717308
BF307939ZSCAN304102183287004832870148GNB1102392117472011770678
BE140587GNB11869117182781718329ELF3691241201984416201984471
BF203707ZSCAN305104183287004832870148GNB1104395117472011770678
BQ228847GNB11179117706541822413DDX50175862107067006170673939
BF203521ZSCAN302105183287004832870151GNB1105397117472011770678
EL955244GNB15424117167291717148PEX241551487789582077895920
DA668677LUZP115212349525923495310GNB151559117358771770679
DA852189RABGEF1112276614712466147245GNB1121546117472391811343
AI933070GNB127198117308321731003GNB1187438117297241729981
AA651630GNB1572117170391717106GNB167410117171011717447
BE537940GNB1199249117171041717154DAD1249575142304409323058136
CA434461GNB118328117167251717033CPLX13093334784965784989
W26101GNB113267117176751717927GNB1260477117472671763711
AA603331GNB120497117167251717201FANK149461010127605008127605124
BF806121EPCAM1133824760123647601569GNB1330582117182521718504
BI026317GNB144239118090041809197LCP1232425134670016346700355
BI022537GNB11270117168281716886GNB167212117167451716890
DA645137SNHG317412883255628834672GNB174461117359961770678
DB357327GNB19134117167291716854CCND1123568116946734469467796
H53458ZFP14182193682734436827511GNB164309117512881751530
BI862769GNB169159117174041717496GNB1158232117173441717418
U67319GNB11181118123701812550CASP7182260110115439699115490662
AV717096MORF4L21229X102935090102935318GNB1210230117780271778047
BC013646GNB1215268117171011717154DAD1268959142303380523058136
AA864236GNB12109117167291716836TARDBP10455611108245411082905
BG315176MBP5160187472505074725205GNB1157272117183991718782
AA650206GNB1874117170391717106GNB169463117171011717495
BE386644GNB11425117359731756884RPL244256353101404661101405535
BF510743KAZN12111533354915333569GNB13473118193511819821

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      
GAIN (# sample)                 
LOSS (# sample)          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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr1:1756861-1756861p.A11G2
chr1:1735946-1735946p.C114C2
chr1:1721903-1721903p.L210L2
chr1:1737942-1737942p.I80T2
chr1:1722014-1722014p.T173T1
chr1:1720557-1720557p.L284R1
chr1:1737959-1737959p.S74S1
chr1:1721845-1721845p.N230Y1
chr1:1735886-1735886p.R134R1
chr1:1720561-1720561p.R283C1

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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
# sample41 71 2 2 1311  11 4
# mutation51 61 2 2 1311  11 4
nonsynonymous SNV51 31 2 2 121    1 3
synonymous SNV   3       1 1  1  1
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
chr1:1756837p.R19L,GNB12
chr1:1718847p.S216G,GNB12
chr1:1747228p.M162T,GNB11
chr1:1720602p.G15C,GNB11
chr1:1721936p.L161L,GNB11
chr1:1749278p.C14C,GNB11
chr1:1720623p.E160K,GNB11
chr1:1721939p.R96H,GNB11
chr1:1749311p.D158N,GNB11
chr1:1720625p.S74S,GNB11

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 GNB1 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 GNB1

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

CDC42,CLSTN1,DNAJC11,GNB1,ICMT,EMC1,CEP104,
KIF1B,LZIC,MFN2,MTOR,NADK,NMNAT1,NOL9,
PANK4,SLC35E2,TCEB3,TPRG1L,UBE4B,UBR4,VAMP3
ANXA5,ARL2BP,CAP1,CREBL2,EFEMP1,FKBP9,FUCA2,
GNA12,GNB1,GNG12,KDELR3,MSN,CPQ,PLS3,
RALB,RHOA,SEPT2,SLC25A43,SLC35B4,ST7,YWHAB

SZRD1,CAPZB,ECE1,FBXO42,GNB1,ICMT,CEP104,
MFN2,MUL1,NADK,PANK4,PINK1,PLEKHM2,RER1,
RNF11,RRAGC,SDF4,SKI,STX12,TPRG1L,WASF2
ABHD6,ALPI,ANPEP,CDHR2,CHRNA7,FAM102A,GNB1,
SLC52A1,GSK3A,HEBP1,INPP5J,ITPK1,CERS2,MEP1A,
MSRA,MYO1A,OIT3,PLA2G12B,PPP2R5D,SEMA3B,USH1G
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 GNB1
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
DB07752guanine nucleotide binding protein (G protein), beta polypeptide 1experimentalFARNESYL
DB00945guanine nucleotide binding protein (G protein), beta polypeptide 1approvedAcetylsalicylic acid
DB00394guanine nucleotide binding protein (G protein), beta polypeptide 1approvedBeclomethasone
DB00443guanine nucleotide binding protein (G protein), beta polypeptide 1approvedBetamethasone
DB01222guanine nucleotide binding protein (G protein), beta polypeptide 1approved; investigationalBudesonide
DB01410guanine nucleotide binding protein (G protein), beta polypeptide 1approved; investigationalCiclesonide
DB01260guanine nucleotide binding protein (G protein), beta polypeptide 1approved; investigationalDesonide
DB01234guanine nucleotide binding protein (G protein), beta polypeptide 1approved; investigationalDexamethasone
DB00180guanine nucleotide binding protein (G protein), beta polypeptide 1approved; investigationalFlunisolide
DB00588guanine nucleotide binding protein (G protein), beta polypeptide 1approved; investigationalFluticasone Propionate
DB00741guanine nucleotide binding protein (G protein), beta polypeptide 1approvedHydrocortisone
DB00959guanine nucleotide binding protein (G protein), beta polypeptide 1approvedMethylprednisolone
DB00764guanine nucleotide binding protein (G protein), beta polypeptide 1approvedMometasone
DB01384guanine nucleotide binding protein (G protein), beta polypeptide 1approvedParamethasone
DB00860guanine nucleotide binding protein (G protein), beta polypeptide 1approvedPrednisolone
DB00635guanine nucleotide binding protein (G protein), beta polypeptide 1approvedPrednisone
DB00896guanine nucleotide binding protein (G protein), beta polypeptide 1approvedRimexolone
DB00620guanine nucleotide binding protein (G protein), beta polypeptide 1approvedTriamcinolone
DB00125guanine nucleotide binding protein (G protein), beta polypeptide 1approved; nutraceuticalL-Arginine
DB00155guanine nucleotide binding protein (G protein), beta polypeptide 1approved; nutraceuticalL-Citrulline
DB00435guanine nucleotide binding protein (G protein), beta polypeptide 1approvedNitric Oxide
DB00988guanine nucleotide binding protein (G protein), beta polypeptide 1approvedDopamine
DB00171guanine nucleotide binding protein (G protein), beta polypeptide 1approved; nutraceuticalAdenosine triphosphate
DB00131guanine nucleotide binding protein (G protein), beta polypeptide 1approved; nutraceuticalAdenosine monophosphate
DB00396guanine nucleotide binding protein (G protein), beta polypeptide 1approvedProgesterone


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Cross referenced IDs for GNB1
* 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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