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 PDE2A

Basic gene info.	Gene symbol	PDE2A
	Gene name	phosphodiesterase 2A, cGMP-stimulated
	Synonyms	CGS-PDE\|PDE2A1\|PED2A4\|cGSPDE
	Cytomap	UCSC genome browser: 11q13.4
	Genomic location	chr11 :72287183-72353504
	Type of gene	protein-coding
	RefGenes	NM_001143839.3, NM_001146209.2,NM_001243784.1,NM_002599.4,
	Ensembl id	ENSG00000186642
	Description	cGMP-dependent 3',5'-cyclic phosphodiesterasecGMP-stimulated phosphodiesterase 1cGMP-stimulated phosphodiesterase 4cyclic GMP-stimulated phosphodiesterase
	Modification date	20141207
dbXrefs	MIM : 602658
	HGNC : HGNC
	Ensembl : ENSG00000186642
	HPRD : 04041
	Vega : OTTHUMG00000102045
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PDE2A
	BioGPS: 5138
	Gene Expression Atlas: ENSG00000186642
	The Human Protein Atlas: ENSG00000186642
Pathway	NCI Pathway Interaction Database: PDE2A
	KEGG: PDE2A
	REACTOME: PDE2A
	ConsensusPathDB
	Pathway Commons: PDE2A
Metabolism	MetaCyc: PDE2A
	HUMANCyc: PDE2A
Regulation	Ensembl's Regulation: ENSG00000186642
	miRBase: chr11 :72,287,183-72,353,504
	TargetScan: NM_001143839
	cisRED: ENSG00000186642
Context	iHOP: PDE2A
	cancer metabolism search in PubMed: PDE2A
	UCL Cancer Institute: PDE2A
Assigned class in ccmGDB	C

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Phenotypic Information for PDE2A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PDE2A
	Familial Cancer Database: PDE2A

* 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
KEGG_PURINE_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: PDE2A
	MedGen: PDE2A (Human Medical Genetics with Condition)
	ClinVar: PDE2A
Phenotype	MGI: PDE2A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PDE2A

Mutations for PDE2A

* 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

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 PDE2A 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
BE938766	PDE2A	40	397	11	72289973	72291982	KIAA1841	393	522	2	61315953	61316082
BQ677895	CAMTA2	265	698	17	4873303	4875682	PDE2A	699	720	11	72305786	72305807
BE924919	CAPZB	1	199	1	19665741	19665940	PDE2A	186	266	11	72323711	72323798
AB209076	KCNIP3	1	3658	2	95963086	95979644	PDE2A	3653	4512	11	72361084	72361943

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=3

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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=25)

Stat. for Deletions (# total SNVs=2)	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
chr11:72301503-72301503	p.T224I	3
chr11:72295734-72295734	p.A466A	2
chr11:72296617-72296617	p.K401N	2
chr11:72300219-72300219	p.S313S	2
chr11:72300239-72300239	p.Q307*	2
chr11:72290629-72290629	p.I735M	2
chr11:72297129-72297129	p.L389L	2
chr11:72385235-72385235	p.G6D	2
chr11:72292005-72292005	p.I686I	2
chr11:72289528-72289528	p.G834R	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=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	3		10	1		2		3			11	6	2		2	16	12		12
# mutation	1	3		11	1		2		3			12	6	2		2	18	12		14
nonsynonymous SNV	1	2		7	1				3			7	4	2		2	14	8		11
synonymous SNV		1		4			2					5	2				4	4		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
chr11:72296617	p.K394N,PDE2A	2
chr11:72289292	p.T812T,PDE2A	2
chr11:72290417	p.A542T,PDE2A	2
chr11:72292005	p.I679I,PDE2A	2
chr11:72289953	p.R749H,PDE2A	2
chr11:72295250	p.A860V,PDE2A	2
chr11:72291952	p.I738I,PDE2A	1
chr11:72296417	p.D607E,PDE2A	1
chr11:72292949	p.E449E,PDE2A	1
chr11:72300277	p.P284S,PDE2A	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 PDE2A 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 PDE2A

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


ADCY4,AOC3,ARHGEF15,BMX,CCL14,CD300LG,CD34, CDH5,CXorf36,ERG,GPIHBP1,GPR146,LDB2,MMRN2, NPR1,PDE2A,PEAR1,ROBO4,S1PR1,SDPR,VWF	ABHD6,ARHGEF15,BMP6,BTNL9,CD300LG,CDH5,CXorf36, EPAS1,ERG,FGD5,GIMAP6,GNAZ,KIAA1462,MMRN2, NRP1,PDE2A,PTPRM,ROBO4,TEK,TENC1,VWF

ABCC9,ANK2,AOC3,CACNA2D1,CCDC69,CCL14,CLIP3, ACKR1,FAM13C,FILIP1,JAM2,NPR1,PDE2A,RBMS3, S1PR1,SDPR,SLC9A9,SPARCL1,SV2B,TLL1,ZEB1	AOC3,ATP1A2,CD109,CLIP3,CPXM2,FAM127C,FBXL7, GJC2,LOXL4,MPP2,NLGN1,NPTXR,PCDHGB7,PDE2A, RBFOX2,RGAG4,RGMA,SEMA4C,SLC29A1,TGFB1I1,TSPAN18

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 PDE2A

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB02315	phosphodiesterase 2A, cGMP-stimulated	experimental	Cyclic Guanosine Monophosphate
DB07954	phosphodiesterase 2A, cGMP-stimulated	experimental	3-ISOBUTYL-1-METHYLXANTHINE
DB08811	phosphodiesterase 2A, cGMP-stimulated	approved	Tofisopam
DB00131	phosphodiesterase 2A, cGMP-stimulated	approved; nutraceutical	Adenosine monophosphate
DB00125	phosphodiesterase 2A, cGMP-stimulated	approved; nutraceutical	L-Arginine
DB00155	phosphodiesterase 2A, cGMP-stimulated	approved; nutraceutical	L-Citrulline
DB00435	phosphodiesterase 2A, cGMP-stimulated	approved	Nitric Oxide
DB01151	phosphodiesterase 2A, cGMP-stimulated	approved	Desipramine
DB00472	phosphodiesterase 2A, cGMP-stimulated	approved	Fluoxetine

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Cross referenced IDs for PDE2A

* 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