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 PRKAA2

Basic gene info.	Gene symbol	PRKAA2
	Gene name	protein kinase, AMP-activated, alpha 2 catalytic subunit
	Synonyms	AMPK\|AMPK2\|AMPKa2\|PRKAA
	Cytomap	UCSC genome browser: 1p31
	Genomic location	chr1 :57110989-57181008
	Type of gene	protein-coding
	RefGenes	NM_006252.3,
	Ensembl id	ENSG00000162409
	Description	5'-AMP-activated protein kinase catalytic subunit alpha-25'-AMP-activated protein kinase, catalytic alpha-2 chainACACA kinaseAMP-activated protein kinase alpha-2 subunit variant 2AMP-activated protein kinase alpha-2 subunit variant 3AMPK alpha 2AMPK
	Modification date	20141207
dbXrefs	MIM : 600497
	HGNC : HGNC
	Ensembl : ENSG00000162409
	HPRD : 02735
	Vega : OTTHUMG00000008282
Protein	UniProt: P54646 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRKAA2
	BioGPS: 5563
	Gene Expression Atlas: ENSG00000162409
	The Human Protein Atlas: ENSG00000162409
Pathway	NCI Pathway Interaction Database: PRKAA2
	KEGG: PRKAA2
	REACTOME: PRKAA2
	ConsensusPathDB
	Pathway Commons: PRKAA2
Metabolism	MetaCyc: PRKAA2
	HUMANCyc: PRKAA2
Regulation	Ensembl's Regulation: ENSG00000162409
	miRBase: chr1 :57,110,989-57,181,008
	TargetScan: NM_006252
	cisRED: ENSG00000162409
Context	iHOP: PRKAA2
	cancer metabolism search in PubMed: PRKAA2
	UCL Cancer Institute: PRKAA2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PRKAA2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PRKAA2
	Familial Cancer Database: PRKAA2

* 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	600497; gene.
Orphanet
Disease	KEGG Disease: PRKAA2
	MedGen: PRKAA2 (Human Medical Genetics with Condition)
	ClinVar: PRKAA2
Phenotype	MGI: PRKAA2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PRKAA2

Mutations for PRKAA2

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PRKAA2	chr1	57158877	57158897	PPP2R1A	chr19	52695828	52695848

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 PRKAA2 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

AI732856

PRKAA2

415

57169907

57171911

PRKAA2

412

471

57171934

57171993

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=64)	Stat. for Synonymous SNVs (# total SNVs=17)

Stat. for Deletions (# total SNVs=6)	Stat. for Insertions (# total SNVs=1)

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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
chr1:57161759-57161759	p.R239C	3
chr1:57157094-57157094	p.F90fs*3	3
chr1:57170075-57170075	p.R407Q	3
chr1:57173294-57173294	p.S523G	3
chr1:57173243-57173243	p.T506A	3
chr1:57159485-57159485	p.G175R	2
chr1:57169966-57169966	p.P371T	2
chr1:57157066-57157066	p.?	2
chr1:57169726-57169726	p.E291K	2
chr1:57171868-57171868	p.L466P	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=5

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		16			3					8	4	3		1	24	8		9
# mutation	3	2		17			3					8	4	3		1	25	9		13
nonsynonymous SNV	3	2		12			2					5	4	2		1	19	6		10
synonymous SNV				5			1					3		1			6	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
chr1:57173243	p.T506A	3
chr1:57171796	p.R239C	2
chr1:57161759	p.M352I	2
chr1:57169756	p.E168K	2
chr1:57173245	p.S377N	2
chr1:57169985	p.R407Q	2
chr1:57170075	p.E301K	2
chr1:57158174	p.T506T	2
chr1:57169911	p.R439C	2
chr1:57159464	p.R442K	2

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 PRKAA2 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 PRKAA2

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


ACLY,AR,C1orf168,C9orf152,DPY19L3,EDEM3,GALNT7, GCC2,GDPD1,LCOR,LRRC8B,MUC5B,MYSM1,NSF, PRKAA2,SECISBP2L,SLC44A4,SPATA6,TRIP11,UCP3,YPEL2	ASB14,ASB4,BEST3,CAPN3,CMYA5,IP6K3,JPH1, KCNQ5,MYBPC1,MYLK3,MYLK4,MYOM2,MYOZ2,OBSCN, PHKA1,PPP2R3A,PRKAA2,SYNPO2L,TXLNB,UGT3A1,WDR62

ASAP1,DYNLRB2,ETNK2,GFRA3,HFM1,HOOK3,HSF1, LAPTM4B,LRRC14,PRKAA2,PTP4A3,RB1CC1,SCRIB,TSNARE1, UBR5,ZFP41,ZNF34,ZNF517,ZNF696,ZNF707,ZSCAN10	AMOTL1,ARHGAP10,CLMP,CPED1,CAP2,DCBLD2,EML1, MAPK4,MSRB3,NPHP1,PALLD,PARD6G,PKD2,PRKAA2, PTMS,SOBP,SORBS2,SUSD4,TMEM47,ZAK,ZMYND11

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 PRKAA2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P54646; -.
Chemistry	ChEMBL	CHEMBL2116; -.
Chemistry	GuidetoPHARMACOLOGY	1542; -.
Organism-specific databases	PharmGKB	PA33745; -.
Organism-specific databases	CTD	5563; -.

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

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Cross referenced IDs for PRKAA2

* 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