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 GNAQ
Basic gene info.Gene symbolGNAQ
Gene nameguanine nucleotide binding protein (G protein), q polypeptide
SynonymsCMC1|G-ALPHA-q|GAQ|SWS
CytomapUCSC genome browser: 9q21
Genomic locationchr9 :80335190-80646219
Type of geneprotein-coding
RefGenesNM_002072.4,
Ensembl idENSG00000156052
Descriptionguanine nucleotide-binding protein G(q) subunit alphaguanine nucleotide-binding protein alpha-q
Modification date20141222
dbXrefs MIM : 600998
HGNC : HGNC
Ensembl : ENSG00000156052
HPRD : 02998
Vega : OTTHUMG00000020059
ProteinUniProt: P50148
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GNAQ
BioGPS: 2776
Gene Expression Atlas: ENSG00000156052
The Human Protein Atlas: ENSG00000156052
PathwayNCI Pathway Interaction Database: GNAQ
KEGG: GNAQ
REACTOME: GNAQ
ConsensusPathDB
Pathway Commons: GNAQ
MetabolismMetaCyc: GNAQ
HUMANCyc: GNAQ
RegulationEnsembl's Regulation: ENSG00000156052
miRBase: chr9 :80,335,190-80,646,219
TargetScan: NM_002072
cisRED: ENSG00000156052
ContextiHOP: GNAQ
cancer metabolism search in PubMed: GNAQ
UCL Cancer Institute: GNAQ
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for GNAQ(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GNAQ
Familial Cancer Database: GNAQ
* 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 163000; phenotype.
185300; phenotype.
600998; gene.
Orphanet 3205; Sturge-Weber syndrome.
624; Familial multiple nevi flammei.
DiseaseKEGG Disease: GNAQ
MedGen: GNAQ (Human Medical Genetics with Condition)
ClinVar: GNAQ
PhenotypeMGI: GNAQ (International Mouse Phenotyping Consortium)
PhenomicDB: GNAQ

Mutations for GNAQ
* 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
breastGNAQchr98049278380492783GNAQchr98050122880501228
ovaryGNAQchr98035201580352035GNAQchr98035250680352526
ovaryGNAQchr98039226580392285chr98032717580327195
ovaryGNAQchr98050231080502330chr98030620580306225
ovaryGNAQchr98059173080591750chr98079542680795446
pancreasGNAQchr98048044380480463TMTC1chr122970956229709582
pancreasGNAQchr98048082880480848chr122541291125412931
pancreasGNAQchr98048082980480849chr122541291125412931
pancreasGNAQchr98050086180500881chr98142218681422206
pancreasGNAQchr98051549780515517GNAQchr98050637480506394
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 GNAQ related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB494590PALM211629112629822112642962GNAQ16050898043052180537263
DA490542GNAQ131998033344080333757DYNC1I23115502172571855172582473
AA729462GNAQ821098049027480490477GNAQ20630498049047080490568
BI021299GNAQ132698058969180590016CELF2323405101128843111288513

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 # sample11 2      1      
GAIN (# sample)11        1      
LOSS (# sample)   2             
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=385

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=344)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr9:80409488-80409488p.Q209P233
chr9:80412493-80412493p.R183Q11
chr9:80409488-80409489p.Q209L6
chr9:80409487-80409487p.Q209H3
chr9:80412517-80412517p.T175M2
chr9:80412518-80412518p.T175S2
chr9:80336317-80336317p.T334T2
chr9:80537092-80537092p.K102N2
chr9:80537112-80537112p.T96S2
chr9:80336284-80336284p.K345N1

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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
# sample 1 10  1    211  54 5
# mutation 1 9  1    211  54 5
nonsynonymous SNV 1 8       2 1  41 2
synonymous SNV   1  1     1   13 3
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
chr9:80412518p.T175S2
chr9:80336301p.X360X1
chr9:80412493p.K345K1
chr9:80537187p.L164F1
chr9:80336317p.V340L1
chr9:80412496p.R148R1
chr9:80537207p.T334T1
chr9:80336387p.D146H1
chr9:80412499p.K311T1
chr9:80537224p.L135V1

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 GNAQ 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 GNAQ

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

ATF7,BAZ2B,BMPR2,PCNXL4,ERCC6L2,TMEM245,INIP,
CREB1,DMXL1,FAM122A,GNAQ,ISCA1,RAB14,SP1,
SPIN1,SPTLC1,STAM2,TSTD2,VPS13A,ZNF484,ZNF510
AKAP11,APPBP2,BMPR2,CDC73,DCUN1D4,DIS3,FAM172A,
FAM8A1,GNAQ,MTMR2,ICE2,OSBPL8,PJA2,PKN2,
RAB11FIP2,RNF180,SACM1L,SMAD2,VAMP4,VPS41,ZHX1

AKAP5,ATP2A3,BCAS1,SMIM14,CAMK2D,CASP7,EDEM3,
EIF4E3,GALNT12,GALNT7,GNAQ,GNE,IKZF2,LOC100129034,
MAP3K5,MIA3,MRAP2,PTAR1,RAB27A,SGMS2,TC2N
AAK1,AFF4,B4GALT5,CLTC,CTNND1,CXorf23,ETV6,
FNDC3B,FOXO3,GNAQ,HERC3,MAPK1,MED13,MXI1,
NPEPPS,PAFAH1B1,PAK2,RAPGEF2,SLC38A1,SMCHD1,VCPIP1
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 GNAQ
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA174; -.
Organism-specific databasesCTD 2776; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00864guanine nucleotide binding protein (G protein), q polypeptideapproved; investigationalTacrolimus
DB00171guanine nucleotide binding protein (G protein), q polypeptideapproved; nutraceuticalAdenosine triphosphate
DB00131guanine nucleotide binding protein (G protein), q polypeptideapproved; nutraceuticalAdenosine monophosphate
DB00125guanine nucleotide binding protein (G protein), q polypeptideapproved; nutraceuticalL-Arginine
DB00155guanine nucleotide binding protein (G protein), q polypeptideapproved; nutraceuticalL-Citrulline
DB00435guanine nucleotide binding protein (G protein), q polypeptideapprovedNitric Oxide
DB00608guanine nucleotide binding protein (G protein), q polypeptideapprovedChloroquine


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Cross referenced IDs for GNAQ
* 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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