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 PDE3B

Basic gene info.	Gene symbol	PDE3B
	Gene name	phosphodiesterase 3B, cGMP-inhibited
	Synonyms	HcGIP1\|cGIPDE1
	Cytomap	UCSC genome browser: 11p15.1
	Genomic location	chr11 :14665268-14893604
	Type of gene	protein-coding
	RefGenes	NM_000922.3,
	Ensembl id	ENSG00000261923
	Description	CGI-PDE BCGIP1cGMP-inhibited 3',5'-cyclic phosphodiesterase Bcyclic GMP-inhibited phosphodiesterase Bcyclic nucleotide phosphodiesterase
	Modification date	20141207
dbXrefs	MIM : 602047
	HGNC : HGNC
	Ensembl : ENSG00000152270
	HPRD : 03626
	Vega : OTTHUMG00000165898
Protein	UniProt: Q13370 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PDE3B
	BioGPS: 5140
	Gene Expression Atlas: ENSG00000261923
	The Human Protein Atlas: ENSG00000261923
Pathway	NCI Pathway Interaction Database: PDE3B
	KEGG: PDE3B
	REACTOME: PDE3B
	ConsensusPathDB
	Pathway Commons: PDE3B
Metabolism	MetaCyc: PDE3B
	HUMANCyc: PDE3B
Regulation	Ensembl's Regulation: ENSG00000261923
	miRBase: chr11 :14,665,268-14,893,604
	TargetScan: NM_000922
	cisRED: ENSG00000261923
Context	iHOP: PDE3B
	cancer metabolism search in PubMed: PDE3B
	UCL Cancer Institute: PDE3B
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PDE3B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PDE3B
	Familial Cancer Database: PDE3B

* 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	602047; gene.
Orphanet
Disease	KEGG Disease: PDE3B
	MedGen: PDE3B (Human Medical Genetics with Condition)
	ClinVar: PDE3B
Phenotype	MGI: PDE3B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PDE3B

Mutations for PDE3B

* 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
ovary	PDE3B	chr11	14849898	14849918		chr23	73796772	73796792
ovary	PDE3B	chr11	14863139	14863339		chr23	73796878	73797078
pancreas	PDE3B	chr11	14714587	14714787		chr11	15073088	15073288
pancreas	PDE3B	chr11	14714680	14714700		chr11	15073977	15073997
pancreas	PDE3B	chr11	14715045	14715245		chr11	15073872	15074072
pancreas	PDE3B	chr11	14715127	14715147		chr11	15073157	15073177

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 PDE3B 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
AI969380	SPATA8	1	228	15	97328609	97328836	PDE3B	223	412	11	14666444	14793516
AI651372	SPATA8	1	228	15	97328609	97328836	PDE3B	223	460	11	14666396	14793516

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=82)	Stat. for Synonymous SNVs (# total SNVs=19)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr11:14865418-14865418	p.S789L	4
chr11:14839801-14839801	p.R532Q	3
chr11:14880728-14880728	p.I887S	2
chr11:14839900-14839900	p.Y565C	2
chr11:14880774-14880774	p.L902L	2
chr11:14666364-14666364	p.L248P	2
chr11:14808095-14808095	p.R381Q	2
chr11:14856585-14856585	p.R755L	2
chr11:14808117-14808117	p.G388G	2
chr11:14889184-14889184	p.G1007S	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=4

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	4	3		12	3				3			12	5			1	6	14		10
# mutation	4	3		12	3				3			13	5			1	6	16		15
nonsynonymous SNV	1	2		7	3				3			12	4			1	5	14		10
synonymous SNV	3	1		5								1	1				1	2		5

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
chr11:14865418	p.S789L	3
chr11:14808095	p.R381Q	2
chr11:14856585	p.R755L	2
chr11:14839801	p.R532Q	2
chr11:14840702	p.D563E	1
chr11:14880728	p.L746I	1
chr11:14665692	p.N869S	1
chr11:14793532	p.S385G	1
chr11:14854289	p.S573N	1
chr11:14889224	p.W750C	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 PDE3B 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 PDE3B

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


ABCD2,ACVR1C,ADH1A,ADH1B,ADIPOQ,AQPEP,CD28, CELF2,CHRDL1,DOCK11,FLI1,GVINP1,IKZF1,KBTBD8, KCNIP2,KLB,LOC339524,PDE3B,PLIN1,PTPRC,SLC19A3	ABCD2,ACO1,ADIPOQ,ANO6,AQPEP,CAT,GYG2, HEPACAM,HRASLS5,KCNIP2,LPL,MARC1,PDE3B,PECR, PEX19,PLIN1,PPARG,PPP2R5A,PRKAR2B,SIK2,SLC16A7

ARID4A,ATAD2B,BMPR2,CHD9,EPM2AIP1,GAB1,GPR125, KIDINS220,KLHL24,LPHN3,PBRM1,PDCD4,PDE3B,PHC3, PIK3C2A,PRKACB,SATB1,SNX30,SOS2,TEAD1,ZBED5	ABI2,ADARB1,VSTM4,C3orf58,CRYBG3,DCBLD2,FOXJ2, JMY,LOC92249,MTMR9,NFIA,PDE3B,PDE5A,POU3F4, PTGS1,RABGAP1,RBFOX2,RNF38,SATB1,SEMA3C,SETBP1

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 PDE3B

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q13370; -.
Chemistry	ChEMBL	CHEMBL2095153; -.
Chemistry	GuidetoPHARMACOLOGY	1299; -.
Organism-specific databases	PharmGKB	PA33127; -.
Organism-specific databases	CTD	5140; -.

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
DB01640	phosphodiesterase 3B, cGMP-inhibited	experimental	(5r)-6-(4-{[2-(3-Iodobenzyl)-3-Oxocyclohex-1-En-1-Yl]Amino}Phenyl)-5-Methyl-4,5-Dihydropyridazin-3(2h)-One
DB01970	phosphodiesterase 3B, cGMP-inhibited	experimental	Hg9a-9, Nonanoyl-N-Hydroxyethylglucamide
DB07954	phosphodiesterase 3B, cGMP-inhibited	experimental	3-ISOBUTYL-1-METHYLXANTHINE
DB00131	phosphodiesterase 3B, cGMP-inhibited	approved; nutraceutical	Adenosine monophosphate
DB00125	phosphodiesterase 3B, cGMP-inhibited	approved; nutraceutical	L-Arginine
DB00155	phosphodiesterase 3B, cGMP-inhibited	approved; nutraceutical	L-Citrulline
DB00435	phosphodiesterase 3B, cGMP-inhibited	approved	Nitric Oxide

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Cross referenced IDs for PDE3B

* 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