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 PDE7B

Basic gene info.	Gene symbol	PDE7B
	Gene name	phosphodiesterase 7B
	Synonyms	bA472E5.1
	Cytomap	UCSC genome browser: 6q23-q24
	Genomic location	chr6 :136172833-136516709
	Type of gene	protein-coding
	RefGenes	NM_018945.3,
	Ensembl id	ENSG00000171408
	Description	cAMP-specific 3',5'-cyclic phosphodiesterase 7Bhigh-affinity cAMP-specific 3',5'-cyclic phosphodiesteraserolipram-insensitive phosphodiesterase type 7
	Modification date	20141207
dbXrefs	MIM : 604645
	HGNC : HGNC
	Ensembl : ENSG00000171408
	HPRD : 06870
	Vega : OTTHUMG00000015641
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PDE7B
	BioGPS: 27115
	Gene Expression Atlas: ENSG00000171408
	The Human Protein Atlas: ENSG00000171408
Pathway	NCI Pathway Interaction Database: PDE7B
	KEGG: PDE7B
	REACTOME: PDE7B
	ConsensusPathDB
	Pathway Commons: PDE7B
Metabolism	MetaCyc: PDE7B
	HUMANCyc: PDE7B
Regulation	Ensembl's Regulation: ENSG00000171408
	miRBase: chr6 :136,172,833-136,516,709
	TargetScan: NM_018945
	cisRED: ENSG00000171408
Context	iHOP: PDE7B
	cancer metabolism search in PubMed: PDE7B
	UCL Cancer Institute: PDE7B
Assigned class in ccmGDB	C

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Phenotypic Information for PDE7B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PDE7B
	Familial Cancer Database: PDE7B

* 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: PDE7B
	MedGen: PDE7B (Human Medical Genetics with Condition)
	ClinVar: PDE7B
Phenotype	MGI: PDE7B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PDE7B

Mutations for PDE7B

* 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	PDE7B	chr6	136453451	136453451	HDAC9	chr7	18127270	18127270
ovary	PDE7B	chr6	136274566	136274586	HS6ST2	chr23	131794493	131794513
ovary	PDE7B	chr6	136381429	136381449		chr1	222187118	222187138
pancreas	PDE7B	chr6	136194361	136194381	MAP3K5	chr6	137013488	137013508
pancreas	PDE7B	chr6	136256095	136256115	MAP7	chr6	136664864	136664884

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 PDE7B 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

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	6	1		1		1					1			1	2		1
GAIN (# sample)	5	1		1		1								1	2		1
LOSS (# sample)	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=32)	Stat. for Synonymous SNVs (# total SNVs=10)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	There's no inserted 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
chr6:136268611-136268611	p.E11K	3
chr6:136495026-136495026	p.T268I	2
chr6:136468578-136468578	p.R86C	2
chr6:136472298-136472298	p.G128E	2
chr6:136429884-136429884	p.R33K	2
chr6:136512841-136512841	p.L406F	2
chr6:136472384-136472384	p.R157*	2
chr6:136494965-136494965	p.R248*	2
chr6:136472385-136472385	p.R157Q	2
chr6:136508200-136508200	p.E358Q	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	1	1		11					1			3	2	2			18	2		6
# mutation	1	1		10					1			3	2	2			17	3		8
nonsynonymous SNV	1	1		5								3	1	2			14	3		6
synonymous SNV				5					1				1				3			2

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
chr6:136268611	p.T268I	3
chr6:136495026	p.E11K	3
chr6:136475307	p.E191D	2
chr6:136468575	p.R248Q	2
chr6:136494966	p.L85F	2
chr6:136472385	p.R157Q	2
chr6:136500196	p.E11G	1
chr6:136429947	p.W337C	1
chr6:136512841	p.D29H	1
chr6:136500203	p.H213H	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 PDE7B 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 PDE7B

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


ADCYAP1R1,CACNA1G,CFH,EBF1,EBF2,EGFLAM,EPHA5, FAT4,GALNT9,GPR124,HGF,IGDCC4,ITM2A,JAM2, LIFR,LPPR4,LRFN5,PDE7B,RHOJ,SEMA3A,TSHZ2	ADAMTS12,ALDH1L2,ARHGAP28,BACE1,BNC2,COL15A1,DCHS1, ENPEP,IGF1,LPPR4,MAP4K4,NID1,NID2,PDE7B, PDGFRB,PEAR1,PHACTR2,RUNX1T1,SPAG9,TBX18,TCF4

A2M,ABCC9,CCDC178,CCM2L,COL14A1,CTSG,ERG, FAM13C,ITPR1,JAM2,MEOX1,PDE2A,PDE7B,PTGDS, S1PR1,SCN4B,SELP,SHE,SIGLEC17P,SV2B,TLL1	ARHGAP31,AVPR2,DSTYK,GALNT11,GPR124,LRRC2,MCC, PDE7B,PDGFRA,PODXL,RANBP6,RCBTB2,RECK,SCN4B, SLC23A2,TEK,WDR91,ZNF337,ZNF471,ZNF74,ZNF84

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 PDE7B

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
DB00651	phosphodiesterase 7B	approved	Dyphylline
DB00920	phosphodiesterase 7B	approved	Ketotifen
DB01151	phosphodiesterase 7B	approved	Desipramine
DB00472	phosphodiesterase 7B	approved	Fluoxetine

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Cross referenced IDs for PDE7B

* 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