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 GNA11

Basic gene info.	Gene symbol	GNA11
	Gene name	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)
	Synonyms	FBH\|FBH2\|FHH2\|GNA-11\|HHC2\|HYPOC2
	Cytomap	UCSC genome browser: 19p13.3
	Genomic location	chr19 :3094407-3121454
	Type of gene	protein-coding
	RefGenes	NM_002067.4,
	Ensembl id	ENSG00000088256
	Description	G-protein subunit alpha-11g alpha-11guanine nucleotide-binding protein G(y) subunit alphaguanine nucleotide-binding protein subunit alpha-11
	Modification date	20141222
dbXrefs	MIM : 139313
	HGNC : HGNC
	Ensembl : ENSG00000088256
	HPRD : 00759
	Vega : OTTHUMG00000180631
Protein	UniProt: P29992 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GNA11
	BioGPS: 2767
	Gene Expression Atlas: ENSG00000088256
	The Human Protein Atlas: ENSG00000088256
Pathway	NCI Pathway Interaction Database: GNA11
	KEGG: GNA11
	REACTOME: GNA11
	ConsensusPathDB
	Pathway Commons: GNA11
Metabolism	MetaCyc: GNA11
	HUMANCyc: GNA11
Regulation	Ensembl's Regulation: ENSG00000088256
	miRBase: chr19 :3,094,407-3,121,454
	TargetScan: NM_002067
	cisRED: ENSG00000088256
Context	iHOP: GNA11
	cancer metabolism search in PubMed: GNA11
	UCL Cancer Institute: GNA11
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for GNA11(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GNA11
	Familial Cancer Database: GNA11

* 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	139313; gene. 145981; phenotype. 615361; phenotype.
Orphanet	101049; Familial hypocalciuric hypercalcemia type 2. 428; Autosomal dominant hypocalcemia.
Disease	KEGG Disease: GNA11
	MedGen: GNA11 (Human Medical Genetics with Condition)
	ClinVar: GNA11
Phenotype	MGI: GNA11 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GNA11

Mutations for GNA11

* 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 GNA11 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
CK818891	GNA11	1	216	19	3115036	3119254	REG1A	208	260	2	79350483	79350535
CK818890	REG1A	16	64	2	79350483	79350531	GNA11	56	272	19	3115035	3119254
BM126302	GNA11	1	200	19	3115052	3119254	REG1A	192	244	2	79350483	79350535
BM126025	REG1A	12	64	2	79350483	79350535	GNA11	56	225	19	3118933	3119254

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=261

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=279)	Stat. for Synonymous SNVs (# total SNVs=12)

Stat. for Deletions (# total SNVs=1)	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
chr19:3118942-3118942	p.Q209L	143
chr19:3115012-3115012	p.R183C	9
chr19:3118942-3118943	p.Q209L	4
chr19:3118941-3118941	p.Q209K	4
chr19:3115011-3115012	p.R183C	3
chr19:3113468-3113468	p.S154S	2
chr19:3113330-3113330	p.A108A	2
chr19:3115013-3115013	p.R183L	2
chr19:3113410-3113410	p.L135P	1
chr19:3121014-3121014	p.R306L	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	7	1				1			3	1	1			7	7		3
# mutation			1	7	1				1			4	1	1			7	7		3
nonsynonymous SNV			1	4					1			3	1	1			4	5		2
synonymous SNV				3	1							1					3	2		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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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
chr19:3113330	p.A108A	2
chr19:3115013	p.A65A	1
chr19:3119342	p.V223A	1
chr19:3110205	p.G66S	1
chr19:3115036	p.L229V	1
chr19:3119345	p.T96T	1
chr19:3110206	p.L254L	1
chr19:3118923	p.S268A	1
chr19:3121014	p.I113I	1
chr19:3110298	p.V269I	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 GNA11 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 GNA11

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


AP3D1,PRRC2B,NOP9,C9orf129,CASZ1,CCNT1,DDI2, GIGYF2,GNA11,HCFC1,HERC2,LMTK2,KMT2B___KMT2D,NACC2, NFIC,PRKAR2A,RREB1,TGFBRAP1,TRIM56,YLPM1,ZNF641	ANKRD11,ATG2A,PRRC2A,PRRC2B,GATC,GCN1L1,GLYR1, GNA11,HERC2,KHSRP,ZSWIM8,NCOR2,OTUD7A,PHF2, POLR3E,PRDM11,RNF216,RPTOR,SUPT6H,TECPR2,ZC3H7B

BTNL8,C9orf129,CNNM4,CORO2A,GNA11,GPT,GUCA2B, JOSD1,KIAA1161,LRP10,LUZP1,NBEAL1,PEX26,PHLPP2, PLEKHA7,PTPRH,RGP1,RREB1,SLC9A1,TTC22,ZZEF1	AGPAT3,MISP,C1orf106,CARD10,COBL,GNA11,KCNK5, KIAA0247,LASP1,LPIN2,LUZP1,MALL,MAST2,MYO5B, MYO7B,PLEKHG6,SCIN,SLC9A3R1,SORT1,SPINT1,TOM1

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 GNA11

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA28764; -.
Organism-specific databases	CTD	2767; -.

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
DB00125	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	approved; nutraceutical	L-Arginine
DB00435	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	approved	Nitric Oxide

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Cross referenced IDs for GNA11

* 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