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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	GNAQ
	Gene name	guanine nucleotide binding protein (G protein), q polypeptide
	Synonyms	CMC1\|G-ALPHA-q\|GAQ\|SWS
	Cytomap	UCSC genome browser: 9q21
	Genomic location	chr9 :80335190-80646219
	Type of gene	protein-coding
	RefGenes	NM_002072.4,
	Ensembl id	ENSG00000156052
	Description	guanine nucleotide-binding protein G(q) subunit alphaguanine nucleotide-binding protein alpha-q
	Modification date	20141222
dbXrefs	MIM : 600998
	HGNC : HGNC
	Ensembl : ENSG00000156052
	HPRD : 02998
	Vega : OTTHUMG00000020059
Protein	UniProt: P50148 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GNAQ
	BioGPS: 2776
	Gene Expression Atlas: ENSG00000156052
	The Human Protein Atlas: ENSG00000156052
Pathway	NCI Pathway Interaction Database: GNAQ
	KEGG: GNAQ
	REACTOME: GNAQ
	ConsensusPathDB
	Pathway Commons: GNAQ
Metabolism	MetaCyc: GNAQ
	HUMANCyc: GNAQ
Regulation	Ensembl's Regulation: ENSG00000156052
	miRBase: chr9 :80,335,190-80,646,219
	TargetScan: NM_002072
	cisRED: ENSG00000156052
Context	iHOP: GNAQ
	cancer metabolism search in PubMed: GNAQ
	UCL Cancer Institute: GNAQ
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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

Cancer 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/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM	163000; phenotype. 185300; phenotype. 600998; gene.
Orphanet	3205; Sturge-Weber syndrome. 624; Familial multiple nevi flammei.
Disease	KEGG Disease: GNAQ
	MedGen: GNAQ (Human Medical Genetics with Condition)
	ClinVar: GNAQ
Phenotype	MGI: GNAQ (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
breast	GNAQ	chr9	80492783	80492783	GNAQ	chr9	80501228	80501228
ovary	GNAQ	chr9	80352015	80352035	GNAQ	chr9	80352506	80352526
ovary	GNAQ	chr9	80392265	80392285		chr9	80327175	80327195
ovary	GNAQ	chr9	80502310	80502330		chr9	80306205	80306225
ovary	GNAQ	chr9	80591730	80591750		chr9	80795426	80795446
pancreas	GNAQ	chr9	80480443	80480463	TMTC1	chr12	29709562	29709582
pancreas	GNAQ	chr9	80480828	80480848		chr12	25412911	25412931
pancreas	GNAQ	chr9	80480829	80480849		chr12	25412911	25412931
pancreas	GNAQ	chr9	80500861	80500881		chr9	81422186	81422206
pancreas	GNAQ	chr9	80515497	80515517	GNAQ	chr9	80506374	80506394

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GNAQ 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
DB494590	PALM2	1	162	9	112629822	112642962	GNAQ	160	508	9	80430521	80537263
DA490542	GNAQ	1	319	9	80333440	80333757	DYNC1I2	311	550	2	172571855	172582473
AA729462	GNAQ	8	210	9	80490274	80490477	GNAQ	206	304	9	80490470	80490568
BI021299	GNAQ	1	326	9	80589691	80590016	CELF2	323	405	10	11288431	11288513

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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)

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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=385

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Somatic 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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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
chr9:80409488-80409488	p.Q209P	233
chr9:80412493-80412493	p.R183Q	11
chr9:80409488-80409489	p.Q209L	6
chr9:80409487-80409487	p.Q209H	3
chr9:80537092-80537092	p.K102N	2
chr9:80537112-80537112	p.T96S	2
chr9:80412517-80412517	p.T175M	2
chr9:80412518-80412518	p.T175S	2
chr9:80336317-80336317	p.T334T	2
chr9:80409441-80409441	p.S225P	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		1		10			1					2	1	1			5	4		5
# mutation		1		9			1					2	1	1			5	4		5
nonsynonymous SNV		1		8								2		1			4	1		2
synonymous SNV				1			1						1				1	3		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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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
chr9:80412518	p.T175S	2
chr9:80430605	p.R183Q	1
chr9:80409488	p.V182A	1
chr9:80430643	p.R181T	1
chr9:80336240	p.X360X	1
chr9:80409502	p.K345K	1
chr9:80537144	p.L164F	1
chr9:80336284	p.V340L	1
chr9:80412465	p.R148R	1
chr9:80537167	p.T334T	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 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

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))

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CNV 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

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


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

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

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA174; -.
Organism-specific databases	CTD	2776; -.

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
DB00864	guanine nucleotide binding protein (G protein), q polypeptide	approved; investigational	Tacrolimus
DB00171	guanine nucleotide binding protein (G protein), q polypeptide	approved; nutraceutical	Adenosine triphosphate
DB00131	guanine nucleotide binding protein (G protein), q polypeptide	approved; nutraceutical	Adenosine monophosphate
DB00125	guanine nucleotide binding protein (G protein), q polypeptide	approved; nutraceutical	L-Arginine
DB00155	guanine nucleotide binding protein (G protein), q polypeptide	approved; nutraceutical	L-Citrulline
DB00435	guanine nucleotide binding protein (G protein), q polypeptide	approved	Nitric Oxide
DB00608	guanine nucleotide binding protein (G protein), q polypeptide	approved	Chloroquine

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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