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 PDE6D
Basic gene info.Gene symbolPDE6D
Gene namephosphodiesterase 6D, cGMP-specific, rod, delta
SynonymsJBTS22|PDED
CytomapUCSC genome browser: 2q35-q36
Genomic locationchr2 :232597146-232645974
Type of geneprotein-coding
RefGenesNM_001291018.1,
NM_002601.3,NR_110994.1,
Ensembl idENSG00000156973
DescriptionGMP-PDE deltaprotein p17retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta
Modification date20141207
dbXrefs MIM : 602676
HGNC : HGNC
Ensembl : ENSG00000156973
HPRD : 04056
Vega : OTTHUMG00000153785
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE6D
BioGPS: 5147
Gene Expression Atlas: ENSG00000156973
The Human Protein Atlas: ENSG00000156973
PathwayNCI Pathway Interaction Database: PDE6D
KEGG: PDE6D
REACTOME: PDE6D
ConsensusPathDB
Pathway Commons: PDE6D
MetabolismMetaCyc: PDE6D
HUMANCyc: PDE6D
RegulationEnsembl's Regulation: ENSG00000156973
miRBase: chr2 :232,597,146-232,645,974
TargetScan: NM_001291018
cisRED: ENSG00000156973
ContextiHOP: PDE6D
cancer metabolism search in PubMed: PDE6D
UCL Cancer Institute: PDE6D
Assigned class in ccmGDBC

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Phenotypic Information for PDE6D(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE6D
Familial Cancer Database: PDE6D
* 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: PDE6D
MedGen: PDE6D (Human Medical Genetics with Condition)
ClinVar: PDE6D
PhenotypeMGI: PDE6D (International Mouse Phenotyping Consortium)
PhenomicDB: PDE6D

Mutations for PDE6D
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
large_intestinePDE6Dchr2232622796232622796chr4183163103183163103
ovaryPDE6Dchr2232611819232611839chr15100299298100299318
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 PDE6D related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BC004322RHBDD239146277551121775518244PDE6D146125972232597140232645986
AJ001626PDE6D15972232597635232645953PDE6D5928322232597697232602809
AV724446ADAMTS413221161168402161168723PDE6D3124652232597175232597328

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
There's no copy number variation information in COSMIC data for this gene.

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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=9)
Stat. for Synonymous SNVs
(# total SNVs=1)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr2:232602845-232602845p.R48H3
chr2:232602765-232602765p.R75C1
chr2:232602769-232602769p.K73fs*151
chr2:232602788-232602788p.S67L1
chr2:232602830-232602830p.I53N1
chr2:232602839-232602839p.P50L1
chr2:232597710-232597710p.D135D1
chr2:232597730-232597730p.I129V1
chr2:232603828-232603828p.P41S1
chr2:232597735-232597735p.V127A1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   3       1    2  3
# mutation   3       1    2  2
nonsynonymous SNV   2       1    2  2
synonymous SNV   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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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
chr2:232602845p.R48H,PDE6D2
chr2:232602846p.S2L,PDE6D1
chr2:232603828p.V127A1
chr2:232645820p.F92F1
chr2:232597735p.R75C,PDE6D1
chr2:232601992p.S67L,PDE6D1
chr2:232602765p.R48S,PDE6D1
chr2:232602788p.P41S,PDE6D1

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 PDE6D 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 PDE6D

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

BCS1L,COPS7B,COX7B,DGUOK,EIF4E2,METTL21A,METTL5,
MFF,MPV17,MRPL18,MTX2,NDUFB3,OST4,PDE6D,
PPP1R7,PTMA,SH3BGRL3,SNRPG,SUMO1,SUMO1P3,ZBTB8OS
ARPC3,C14orf119,C8orf59,DAD1,DYNLT1,ERH,KRTCAP2,
LSM2,MYL12B,PDE6D,PPP1R11,PSENEN,RAC1,RPF1,
SEC61B,SF3B14,SNRPG,SRP14,TOMM6,TXN,TXNDC12

ATRAID,COA5,COPS8,CRIPT,DPY30,GPN1,MFF,
MITD1,MORN2,MYEOV2,NDUFA13,ORC4,PDE6D,PSMA2,
RNF181,RNF25,SNRPG,TMEM126A,TMEM126B,UBL5,USP39
ATP5O,C14orf119,C18orf21,CGRRF1,COMMD3,DCTN3,DPY30,
GOLGA7,IAH1,NDUFA11,NDUFA6,NDUFV2,NSMCE2,PDE6D,
PEX2,PPP1R8,SNX11,SRP14,SUPT4H1,TXNL1,UQCR11
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 PDE6D
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
DB01151phosphodiesterase 6D, cGMP-specific, rod, deltaapprovedDesipramine
DB00472phosphodiesterase 6D, cGMP-specific, rod, deltaapprovedFluoxetine


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Cross referenced IDs for PDE6D
* 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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