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 PDE6B
Basic gene info.Gene symbolPDE6B
Gene namephosphodiesterase 6B, cGMP-specific, rod, beta
SynonymsCSNB3|CSNBAD2|PDEB|RP40|rd1
CytomapUCSC genome browser: 4p16.3
Genomic locationchr4 :619362-664681
Type of geneprotein-coding
RefGenesNM_000283.3,
NM_001145291.1,NM_001145292.1,
Ensembl idENSG00000133256
DescriptionGMP-PDE betarod cGMP-phosphodiesterase beta-subunitrod cGMP-specific 3',5'-cyclic phosphodiesterase subunit beta
Modification date20141219
dbXrefs MIM : 180072
HGNC : HGNC
Ensembl : ENSG00000133256
HPRD : 01571
Vega : OTTHUMG00000159909
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE6B
BioGPS: 5158
Gene Expression Atlas: ENSG00000133256
The Human Protein Atlas: ENSG00000133256
PathwayNCI Pathway Interaction Database: PDE6B
KEGG: PDE6B
REACTOME: PDE6B
ConsensusPathDB
Pathway Commons: PDE6B
MetabolismMetaCyc: PDE6B
HUMANCyc: PDE6B
RegulationEnsembl's Regulation: ENSG00000133256
miRBase: chr4 :619,362-664,681
TargetScan: NM_000283
cisRED: ENSG00000133256
ContextiHOP: PDE6B
cancer metabolism search in PubMed: PDE6B
UCL Cancer Institute: PDE6B
Assigned class in ccmGDBC

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Phenotypic Information for PDE6B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE6B
Familial Cancer Database: PDE6B
* 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: PDE6B
MedGen: PDE6B (Human Medical Genetics with Condition)
ClinVar: PDE6B
PhenotypeMGI: PDE6B (International Mouse Phenotyping Consortium)
PhenomicDB: PDE6B

Mutations for PDE6B
* 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
There's no inter-chromosomal structural variation.
- 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
NSPDE6Bchr4662370662370PDE6Bchr4663658663658
NSPDE6Bchr4663161663161PDE6Bchr4663588663588
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 PDE6B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM725061INO8049311154129112741291389PDE6B3085824664297664571
BU741962PDE6B122864664297664571INO80283545154129112741291389

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 # sample1  1             
GAIN (# sample)1                
LOSS (# sample)   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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=56)
Stat. for Synonymous SNVs
(# total SNVs=31)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr4:619517-619517p.A34A3
chr4:628613-628613p.E206K3
chr4:658005-658005p.I708I3
chr4:619514-619514p.A33A2
chr4:629746-629746p.T233T2
chr4:651213-651213p.R444H2
chr4:656373-656373p.D600N2
chr4:648636-648636p.I317I2
chr4:651263-651263p.D461N2
chr4:619541-619541p.P42P2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample221112 1 32 931  2211 9
# mutation221122 1 32 931  2513 10
nonsynonymous SNV12 82   22 62   1110 4
synonymous SNV1 14  1 1  311  143 6
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
chr4:628613p.E206K,PDE6B3
chr4:652779p.R165H,PDE6B2
chr4:648636p.I38I,PDE6B2
chr4:651213p.C201C,PDE6B2
chr4:649789p.S72S,PDE6B2
chr4:619541p.P42P,PDE6B2
chr4:661714p.A454A,PDE6B1
chr4:628559p.I130I,PDE6B1
chr4:647926p.L14L,PDE6B1
chr4:656917p.F145F,PDE6B1

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 PDE6B 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 PDE6B

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

RRNAD1,C3orf18,C9orf116,CCDC103,CCDC153,CCDC24,CCDC96,
FUZ,GMPR2,HMGCL,LOC348926,LRRC48,MDP1,ZNF205-AS1,
MYL5,NPRL2,PARP3,PDE6B,RAB17,RBKS,THTPA
BSPRY,CBLC,CCDC24,EFNA4,ELMO3,GSTO2,H2AFY2,
MAGEF1,PDE6B,PPAP2C,PRKCZ,PRRG2,RAB25,RTKN,
SPINT1,SPINT2,STXBP2,SYTL1,TMC4,TMEM125,TMPRSS13

BEND4,CD37,CPAMD8,DOCK8,HVCN1,IL16,TP73-AS1,
LIMD2,LRRC4C,LY9,MEOX2,P2RY8,PCDH11X,PDE6B,
POU2F2,PRKCB,PTGDS,RAB39B,RCSD1,TNFSF8,ZNF804A
APOC1,BTK,TMEM243,CD48,CYSLTR1,EVI2A,GLT8D1,
GPSM3,HELQ,KREMEN2,LAPTM5,LOC374443,LOC645431,LY86,
MFNG,PDE6B,RAB33A,RINL,S100Z,SYTL1,ZCCHC7
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 PDE6B


There's no related Drug.
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Cross referenced IDs for PDE6B
* 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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