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 GNG2

Basic gene info.	Gene symbol	GNG2
	Gene name	guanine nucleotide binding protein (G protein), gamma 2
	Synonyms	-
	Cytomap	UCSC genome browser: 14q21
	Genomic location	chr14 :52327021-52436518
	Type of gene	protein-coding
	RefGenes	NM_001243773.1, NM_001243774.1,NM_053064.4,
	Ensembl id	ENSG00000186469
	Description	g gamma-Iguanine nucleotide binding protein gamma 2guanine nucleotide-binding protein G(I)/G(O) gamma-2 subunitguanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
	Modification date	20141207
dbXrefs	MIM : 606981
	HGNC : HGNC
	Ensembl : ENSG00000186469
	HPRD : 16234
	Vega : OTTHUMG00000171083
Protein	UniProt: P59768 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_GNG2
	BioGPS: 54331
	Gene Expression Atlas: ENSG00000186469
	The Human Protein Atlas: ENSG00000186469
Pathway	NCI Pathway Interaction Database: GNG2
	KEGG: GNG2
	REACTOME: GNG2
	ConsensusPathDB
	Pathway Commons: GNG2
Metabolism	MetaCyc: GNG2
	HUMANCyc: GNG2
Regulation	Ensembl's Regulation: ENSG00000186469
	miRBase: chr14 :52,327,021-52,436,518
	TargetScan: NM_001243773
	cisRED: ENSG00000186469
Context	iHOP: GNG2
	cancer metabolism search in PubMed: GNG2
	UCL Cancer Institute: GNG2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GNG2 in cancer cell metabolism	1. Matimba A, Li F, Livshits A, Cartwright CS, Scully S, et al. (2014) Thiopurine pharmacogenomics: association of SNPs with clinical response and functional validation of candidate genes. Pharmacogenomics 15: 433-447. doi: 10.2217/pgs.13.226. pmid: 4027966. go to article 2. Yajima I, Kumasaka MY, Tamura H, Ohgami N, Kato M (2012) Functional analysis of GNG2 in human malignant melanoma cells. J Dermatol Sci 68: 172-178. doi: 10.1016/j.jdermsci.2012.09.009. go to article

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Phenotypic Information for GNG2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: GNG2
	Familial Cancer Database: GNG2

* 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	606981; gene.
Orphanet
Disease	KEGG Disease: GNG2
	MedGen: GNG2 (Human Medical Genetics with Condition)
	ClinVar: GNG2
Phenotype	MGI: GNG2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: GNG2

Mutations for GNG2

* 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 GNG2 related fusion information.

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

BF886210

GNG2

144

52435791

52435921

GNG2

139

192

52435844

52435897

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=9)	Stat. for Synonymous SNVs (# total SNVs=1)

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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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
chr14:52433367-52433367	p.P60S	5
chr14:52433353-52433353	p.P55L	3
chr14:52433368-52433368	p.P60L	1
chr14:52417415-52417415	p.A7T	1
chr14:52433384-52433384	p.K65N	1
chr14:52417471-52417471	p.I25I	1
chr14:52433399-52433399	p.I70I	1
chr14:52417474-52417474	p.D26E	1
chr14:52433402-52433402	p.L71L	1
chr14:52417477-52417477	p.R27S	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=3

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				1							4					5			2
# mutation	1				1							4					3			2
nonsynonymous SNV	1				1							4					1			2
synonymous SNV																	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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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
chr14:52433367	p.P60S,GNG2	3
chr14:52433353	p.P55L,GNG2	2
chr14:52417474	p.D26E,GNG2	1
chr14:52417477	p.R27S,GNG2	1
chr14:52433295	p.D36Y,GNG2	1
chr14:52433336	p.P49P,GNG2	1
chr14:52433361	p.E58Q,GNG2	1
chr14:52433368	p.P60L,GNG2	1
chr14:52433384	p.K65N,GNG2	1
chr14:52433399	p.I70I,GNG2	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 GNG2 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 GNG2

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


APBB1IP,CD200R1,CELF2,DOCK11,ETS1,EVI2A,FLI1, FMNL3,GAB3,GIMAP6,GNG2,KCTD12,LIX1L,MPEG1, PRDM8,RASSF2,SH2B3,SLC9A9,SRGN,WIPF1,ZEB2	ANXA5,ASPH,BHMT2,CAV1,CHRDL1,DOCK11,GNG2, GNS,ITGB1BP1,ITIH5,ITSN1,LAMA4,PALMD,PCDH9, PYGL,RHOQ,SAR1A,SEPT11,SORBS1,STS,VKORC1L1

ARHGEF6,CYSLTR1,DOCK10,FLI1,GIMAP4,GIMAP6,GIMAP7, GNG2,GYPC,ITGA4,LRRC8C,MYO5A,PPP1R16B,PRKCB, RASSF2,RCSD1,SH2D3C,SLC9A9,SYT11,WIPF1,ZIK1	AGTR1,AP1S2,BAI3,BCHE,CADM1,CEND1,CRISPLD1, DDIT4L,DGKB,EID2B,FAM171B,GLRB,GNG2,GYG1, NECAB1,NUDT10,SGCE,SH3BGRL,SSBP2,ZDHHC15,ZDHHC22

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 GNG2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA28784; -.
Organism-specific databases	CTD	54331; -.

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
DB01159	guanine nucleotide binding protein (G protein), gamma 2	approved	Halothane
DB00125	guanine nucleotide binding protein (G protein), gamma 2	approved; nutraceutical	L-Arginine
DB00435	guanine nucleotide binding protein (G protein), gamma 2	approved	Nitric Oxide

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Cross referenced IDs for GNG2

* 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