Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolPDE7B
Gene namephosphodiesterase 7B
SynonymsbA472E5.1
CytomapUCSC genome browser: 6q23-q24
Genomic locationchr6 :136172833-136516709
Type of geneprotein-coding
RefGenesNM_018945.3,
Ensembl idENSG00000171408
DescriptioncAMP-specific 3',5'-cyclic phosphodiesterase 7Bhigh-affinity cAMP-specific 3',5'-cyclic phosphodiesteraserolipram-insensitive phosphodiesterase type 7
Modification date20141207
dbXrefs MIM : 604645
HGNC : HGNC
Ensembl : ENSG00000171408
HPRD : 06870
Vega : OTTHUMG00000015641
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE7B
BioGPS: 27115
Gene Expression Atlas: ENSG00000171408
The Human Protein Atlas: ENSG00000171408
PathwayNCI Pathway Interaction Database: PDE7B
KEGG: PDE7B
REACTOME: PDE7B
ConsensusPathDB
Pathway Commons: PDE7B
MetabolismMetaCyc: PDE7B
HUMANCyc: PDE7B
RegulationEnsembl's Regulation: ENSG00000171408
miRBase: chr6 :136,172,833-136,516,709
TargetScan: NM_018945
cisRED: ENSG00000171408
ContextiHOP: PDE7B
cancer metabolism search in PubMed: PDE7B
UCL Cancer Institute: PDE7B
Assigned class in ccmGDBC

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Phenotypic Information for PDE7B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_PURINE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PDE7B
MedGen: PDE7B (Human Medical Genetics with Condition)
ClinVar: PDE7B
PhenotypeMGI: PDE7B (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastPDE7Bchr6136453451136453451HDAC9chr71812727018127270
ovaryPDE7Bchr6136274566136274586HS6ST2chr23131794493131794513
ovaryPDE7Bchr6136381429136381449chr1222187118222187138
pancreasPDE7Bchr6136194361136194381MAP3K5chr6137013488137013508
pancreasPDE7Bchr6136256095136256115MAP7chr6136664864136664884
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PDE7B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample61 1 1    1  12 1
GAIN (# sample)51 1 1       12 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr6:136268611-136268611p.E11K3
chr6:136495026-136495026p.T268I2
chr6:136468578-136468578p.R86C2
chr6:136472298-136472298p.G128E2
chr6:136429884-136429884p.R33K2
chr6:136512841-136512841p.L406F2
chr6:136472384-136472384p.R157*2
chr6:136494965-136494965p.R248*2
chr6:136508200-136508200p.E358Q2
chr6:136472385-136472385p.R157Q2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample11 11    1  322  182 6
# mutation11 10    1  322  173 8
nonsynonymous SNV11 5       312  143 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr6:136495026p.T268I3
chr6:136268611p.E11K3
chr6:136494966p.L85F2
chr6:136472385p.R157Q2
chr6:136475307p.E191D2
chr6:136468575p.R248Q2
chr6:136468578p.I63I1
chr6:136512924p.H262Y1
chr6:136268612p.L406L1
chr6:136502427p.K67K1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00651phosphodiesterase 7BapprovedDyphylline
DB00920phosphodiesterase 7BapprovedKetotifen
DB01151phosphodiesterase 7BapprovedDesipramine
DB00472phosphodiesterase 7BapprovedFluoxetine


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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



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