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 PRKAG2

Basic gene info.	Gene symbol	PRKAG2
	Gene name	protein kinase, AMP-activated, gamma 2 non-catalytic subunit
	Synonyms	AAKG\|AAKG2\|CMH6\|H91620p\|WPWS
	Cytomap	UCSC genome browser: 7q36.1
	Genomic location	chr7 :151253200-151511957
	Type of gene	protein-coding
	RefGenes	NM_001040633.1, NM_016203.3,NM_024429.1,
	Ensembl id	ENSG00000106617
	Description	5'-AMP-activated protein kinase subunit gamma-2AMPK subunit gamma-2hypothetical protein
	Modification date	20141207
dbXrefs	MIM : 602743
	HGNC : HGNC
	Ensembl : ENSG00000106617
	HPRD : 04119
	Vega : OTTHUMG00000157324
Protein	UniProt: Q9UGJ0 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRKAG2
	BioGPS: 51422
	Gene Expression Atlas: ENSG00000106617
	The Human Protein Atlas: ENSG00000106617
Pathway	NCI Pathway Interaction Database: PRKAG2
	KEGG: PRKAG2
	REACTOME: PRKAG2
	ConsensusPathDB
	Pathway Commons: PRKAG2
Metabolism	MetaCyc: PRKAG2
	HUMANCyc: PRKAG2
Regulation	Ensembl's Regulation: ENSG00000106617
	miRBase: chr7 :151,253,200-151,511,957
	TargetScan: NM_001040633
	cisRED: ENSG00000106617
Context	iHOP: PRKAG2
	cancer metabolism search in PubMed: PRKAG2
	UCL Cancer Institute: PRKAG2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PRKAG2 in cancer cell metabolism	1. Kim M, Hunter RW, Garcia-Menendez L, Gong G, Yang Y-Y, et al. (2014) Mutation in the γ2-subunit of AMP-activated protein kinase stimulates cardiomyocyte proliferation and hypertrophy independent of glycogen storage. Circulation research 114: 966-975. go to article

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Phenotypic Information for PRKAG2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PRKAG2
	Familial Cancer Database: PRKAG2

* 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 REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	194200; phenotype. 261740; phenotype. 600858; phenotype. 602743; gene.
Orphanet	155; Familial isolated hypertrophic cardiomyopathy. 907; Wolff-Parkinson-White syndrome.
Disease	KEGG Disease: PRKAG2
	MedGen: PRKAG2 (Human Medical Genetics with Condition)
	ClinVar: PRKAG2
Phenotype	MGI: PRKAG2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PRKAG2

Mutations for PRKAG2

* 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	PRKAG2	chr7	151378592	151378592	PRKAG2	chr7	151388130	151388130
ovary	PRKAG2	chr7	151260767	151260787		chr19	23755164	23755184
ovary	PRKAG2	chr7	151299470	151299670	MLL3	chr7	151979326	151979526
ovary	PRKAG2	chr7	151368225	151368245	PRKAG2	chr7	151361612	151361632
pancreas	PRKAG2	chr7	151368215	151368235	PRKAG2	chr7	151368268	151368288

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 PRKAG2 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
DB487487	ZNF786	2	72	7	148787715	148787785	PRKAG2	72	446	7	151292454	151372724
DB486204	ZNF786	2	72	7	148787715	148787785	PRKAG2	72	420	7	151292481	151372724
AI766782	ACOX1	30	190	17	73938959	73939119	PRKAG2	184	327	7	151352004	151352146
AK130536	SLC2A13	2	75	12	40416841	40416914	PRKAG2	75	3343	7	151562747	151566014
BP373596	PRKAG2	1	480	7	151257461	151261400	PRKAG2	474	581	7	151269523	151269630
BG007354	PPP3CC	13	283	8	22384338	22384612	PRKAG2	272	373	7	151253966	151254066
BF912904	PRKAG2	24	215	7	151454298	151454489	SMU1	213	364	9	33057606	33060507
BE763984	PRKAG2	1	341	7	151257210	151257549	MALAT1	338	466	11	65266740	65266868

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample		2		2	1		2		2					2	1
GAIN (# sample)		2		2			1		2					2
LOSS (# sample)					1		1								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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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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=49)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=2)

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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
chr7:151269791-151269791	p.Q337R	4
chr7:151257690-151257690	p.V533G	4
chr7:151265922-151265922	p.F371F	3
chr7:151262838-151262838	p.R456Q	3
chr7:151261177-151261177	p.I524K	2
chr7:151372719-151372719	p.S157S	2
chr7:151269770-151269770	p.H344R	2
chr7:151372596-151372597	p.D199fs*56	2
chr7:151372617-151372617	p.I191I	2
chr7:151573690-151573690	p.M6V	2

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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		2	2	7	1		4		4	1		6	3	1			11	6		7
# mutation		2	2	8	1		4		4	1		6	3	1			11	6		6
nonsynonymous SNV		1	2	5	1		2		4	1		5	3	1			8	4		3
synonymous SNV		1		3			2					1					3	2		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
chr7:151262838	p.R215Q,PRKAG2	3
chr7:151372617	p.I147I,PRKAG2	2
chr7:151478258	p.E16Q,PRKAG2	1
chr7:151261232	p.G102S,PRKAG2	1
chr7:151265913	p.T252T,PRKAG2	1
chr7:151483560	p.S15S,PRKAG2	1
chr7:151372540	p.E89Q,PRKAG2	1
chr7:151478262	p.V222G,PRKAG2	1
chr7:151261254	p.L187R,PRKAG2	1
chr7:151265922	p.R72H,PRKAG2	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 PRKAG2 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 PRKAG2

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


ABCF2,ACTR3B,AGK,ARMC10,CASP2,CNOT4,CUL1, DNAJB6,ESYT2,GALNT11,LOC284578,LUC7L2,NUB1,PMPCB, PRKAG2,RAB12,RHEB,RINT1,UBE3C,ZNF398,ZNF862	AASS,BCKDHB,CALCRL,RHOV___CHP1,CRLS1,CYP1A2,DNAH9, GYS2,MAP3K5,MKX,MOGAT1,NAALAD2,PLCXD1,PRKAG2, RNF125,SCML1,ST3GAL6,STK39,STOX1,TGDS,TWIST1

ARPC1A,ASL,BCL7B,TMEM248,CAPZA2,COG5,COL17A1, FIS1,LUZP6,NAPEPLD,ORC5,PNPLA8,PRKAG2,RABGEF1, RHEB,RINT1,SBDS,ST7,SYPL1,TMEM120A,ZNF394	AGR3,ARL5A,AZIN1,CDKN2AIP,CISD1,CRHR1,CYB5A, DPH3,FAM35DP,HACL1,IFT20,LOC202781,MBIP,PAQR3, PIGH,PRKAG2,RARS2,RWDD2A,STARD3NL,TBC1D15,TMEM14A

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 PRKAG2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2096907; -.
Organism-specific databases	PharmGKB	PA33752; -.
Organism-specific databases	CTD	51422; -.

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
DB00131	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	approved; nutraceutical	Adenosine monophosphate
DB00171	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	approved; nutraceutical	Adenosine triphosphate
DB00412	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	approved; investigational	Rosiglitazone
DB01132	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	approved; investigational	Pioglitazone
DB00331	protein kinase, AMP-activated, gamma 2 non-catalytic subunit	approved	Metformin

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Cross referenced IDs for PRKAG2

* 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