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 PDE8B

Basic gene info.	Gene symbol	PDE8B
	Gene name	phosphodiesterase 8B
	Synonyms	ADSD\|PPNAD3
	Cytomap	UCSC genome browser: 5q13.3
	Genomic location	chr5 :76506705-76724080
	Type of gene	protein-coding
	RefGenes	NM_001029851.2, NM_001029852.2,NM_001029853.2,NM_001029854.2,NM_003719.3,
	Ensembl id	ENSG00000113231
	Description	3',5' cyclic nucleotide phosphodiesterase 8Bcell proliferation-inducing gene 22 proteinhigh affinity cAMP-specific and IBMX-insensitive 3',5'-cyclic phosphodiesterase 8BhsPDE8B
	Modification date	20141207
dbXrefs	MIM : 603390
	HGNC : HGNC
	Ensembl : ENSG00000113231
	HPRD : 04546
	Vega : OTTHUMG00000102170
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PDE8B
	BioGPS: 8622
	Gene Expression Atlas: ENSG00000113231
	The Human Protein Atlas: ENSG00000113231
Pathway	NCI Pathway Interaction Database: PDE8B
	KEGG: PDE8B
	REACTOME: PDE8B
	ConsensusPathDB
	Pathway Commons: PDE8B
Metabolism	MetaCyc: PDE8B
	HUMANCyc: PDE8B
Regulation	Ensembl's Regulation: ENSG00000113231
	miRBase: chr5 :76,506,705-76,724,080
	TargetScan: NM_001029851
	cisRED: ENSG00000113231
Context	iHOP: PDE8B
	cancer metabolism search in PubMed: PDE8B
	UCL Cancer Institute: PDE8B
Assigned class in ccmGDB	C

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Phenotypic Information for PDE8B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PDE8B
	Familial Cancer Database: PDE8B

* 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: PDE8B
	MedGen: PDE8B (Human Medical Genetics with Condition)
	ClinVar: PDE8B
Phenotype	MGI: PDE8B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PDE8B

Mutations for PDE8B

* 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	PDE8B	chr5	76513508	76513508	PDE8B	chr5	76722336	76722336
breast	PDE8B	chr5	76722208	76722208	GMDS	chr6	2163549	2163549
ovary	PDE8B	chr5	76521295	76521315	PDE8B	chr5	76508727	76508747
ovary	PDE8B	chr5	76646625	76646645	PDE8B	chr5	76513562	76513582
pancreas	PDE8B	chr5	76691122	76691322	ZNF286A	chr17	15610430	15610630

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 PDE8B 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

M85313

PDE8B

184

76523256

76523439

TERF2IP

173

412

75690999

75691242

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=78)	Stat. for Synonymous SNVs (# total SNVs=26)

Stat. for Deletions (# total SNVs=1)	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
chr5:76703223-76703223	p.R436C	4
chr5:76717755-76717755	p.R787H	2
chr5:76715631-76715631	p.M723I	2
chr5:76621417-76621417	p.A151A	2
chr5:76709105-76709105	p.A628T	2
chr5:76645262-76645262	p.E299K	2
chr5:76700600-76700600	p.S422S	2
chr5:76714204-76714204	p.H688Y	2
chr5:76646938-76646938	p.Q356K	2
chr5:76709015-76709015	p.R598W	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		15	2		7	1	1			11	4	2	1	1	23	6		17
# mutation		1		17	2		7	1	1			11	4	2	1	1	24	6		20
nonsynonymous SNV				13	1		5		1			6	2			1	19	5		19
synonymous SNV		1		4	1		2	1				5	2	2	1		5	1		1

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
chr5:76714063	p.S325S,PDE8B	2
chr5:76700600	p.R339C,PDE8B	2
chr5:76703223	p.S195L,PDE8B	2
chr5:76709015	p.D544N,PDE8B	2
chr5:76624876	p.R501W,PDE8B	2
chr5:76714268	p.A531T,PDE8B	1
chr5:76621481	p.S645N,PDE8B	1
chr5:76646927	p.G35S,PDE8B	1
chr5:76721592	p.R180W,PDE8B	1
chr5:76627229	p.F278F,PDE8B	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 PDE8B 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 PDE8B

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


BBX,LINC00473,ECEL1,EDARADD,ERBB2IP,ERO1LB,EVX1, FKTN,GABRR3,HSDL2,MCTP2,MTUS1,PDE4D,PDE8B, PITX1,PROKR2,SLC6A14,SMAD5,SRFBP1,WDR41,ZBED3	ACO1,AOC3,ASPH,ATP2B4,NPR3,CPED1,CCDC3, COBLL1,ESYT1,FZD5,MDFIC,MYO1C,PALM2-AKAP2,PARVA, PDE8B,PLIN1,PLXNA4,PRKAR2B,PYGL,SLC25A16,VKORC1L1

BPIFB3,NAT16,DCHS2,DDHD1,FAM184A,FMNL3,GPM6B, GREB1,HIP1,ITPR1,TP73-AS1,KRTAP10-11,LOC100272216,MCTP1, MPP2,NPTXR,PDE8B,PPM1K,TXLNB,ZNF483,ZNF671	ASIC1,ATP1A2,C20orf166-AS1,NPR3,FAXDC2,CAMK2G,PIEZO2, FBXL22,RBFOX3,LOC92249,LOXL4,MEIS2,NRK,NRXN2, PDE2A,PDE8B,PLCD4,RGAG4,SLC29A1,SOX11,SRPK3

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 PDE8B

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
DB00920	phosphodiesterase 8B	approved	Ketotifen
DB00472	phosphodiesterase 8B	approved	Fluoxetine

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Cross referenced IDs for PDE8B

* 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