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 PDE10A
Basic gene info.Gene symbolPDE10A
Gene namephosphodiesterase 10A
SynonymsHSPDE10A
CytomapUCSC genome browser: 6q26
Genomic locationchr6 :165740775-166075588
Type of geneprotein-coding
RefGenesNM_001130690.2,
NR_045597.1,NM_006661.2,
Ensembl idENSG00000112541
DescriptioncAMP and cAMP-inhibited cGMP 3',5'-cyclic phosphodiesterase 10AdJ416F21.1 (phosphodiesterase 10A)phosphodiesterase 10A1 (PDE10A1)
Modification date20141218
dbXrefs MIM : 610652
HGNC : HGNC
Ensembl : ENSG00000112541
HPRD : 17828
Vega : OTTHUMG00000015986
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDE10A
BioGPS: 10846
Gene Expression Atlas: ENSG00000112541
The Human Protein Atlas: ENSG00000112541
PathwayNCI Pathway Interaction Database: PDE10A
KEGG: PDE10A
REACTOME: PDE10A
ConsensusPathDB
Pathway Commons: PDE10A
MetabolismMetaCyc: PDE10A
HUMANCyc: PDE10A
RegulationEnsembl's Regulation: ENSG00000112541
miRBase: chr6 :165,740,775-166,075,588
TargetScan: NM_001130690
cisRED: ENSG00000112541
ContextiHOP: PDE10A
cancer metabolism search in PubMed: PDE10A
UCL Cancer Institute: PDE10A
Assigned class in ccmGDBC

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Phenotypic Information for PDE10A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDE10A
Familial Cancer Database: PDE10A
* 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: PDE10A
MedGen: PDE10A (Human Medical Genetics with Condition)
ClinVar: PDE10A
PhenotypeMGI: PDE10A (International Mouse Phenotyping Consortium)
PhenomicDB: PDE10A

Mutations for PDE10A
* 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
ovaryPDE10Achr6165957101165957121CAB39chr2231651940231651960
ovaryPDE10Achr6165957101165957121CAB39chr2231651941231651961
pancreasPDE10Achr6165799859165799879PDE10Achr6165800017165800037
pancreasPDE10Achr6166033121166033141PDE10Achr6166032925166032945
pancreasPDE10Achr6166037479166037499JPXchr237318711573187135
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 PDE10A 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 # sample25 1  4 2 2  2  2
GAIN (# sample)1         1  1   
LOSS (# sample)15 1  4 2 1  1  2
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=127)
Stat. for Synonymous SNVs
(# total SNVs=38)
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
chr6:165809889-165809889p.S436S2
chr6:165863794-165863794p.Q84Q2
chr6:165756970-165756970p.M659I2
chr6:165827045-165827045p.E398*2
chr6:165863797-165863797p.E83D2
chr6:165746585-165746585p.R757*2
chr6:165862431-165862431p.L117L2
chr6:165808737-165808737p.G470C2
chr6:165809911-165809911p.R429Q2
chr6:165846610-165846610p.R172Q2

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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
# sample16 164 14 1  3012411157 10
# mutation17 166 14 1  3113411167 14
nonsynonymous SNV15 145 12 1  278311115 11
synonymous SNV 2 21 2    451  52 3
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
chr6:165863797p.R296C2
chr6:165746557p.R496W2
chr6:165862423p.I382I2
chr6:165808737p.E93D2
chr6:165801865p.G480C2
chr6:165827121p.T441M2
chr6:165863740p.C130Y2
chr6:165806284p.I112I2
chr6:165809905p.S776L2
chr6:165832235p.F503V2

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 PDE10A 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 PDE10A

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

ALOX12,ARNTL2,ATF7IP,C12orf4,C12orf5,CHRNB1,CSGALNACT1,
DCBLD1,DDX52,ECEL1,FXYD7,GOLGA8F,HNF1B,PDE10A,
PPFIBP1,ROS1,TMEM45A,ZNF254,ZNF536,ZNF675,ZNF681
ASAP1,ASAP2,ATP13A3,CLTC,CYSLTR1,DPY19L1,FGF7,
FUT11,HRH1,PAK2,PDE10A,PHACTR2,RAB23,RECQL,
RGL1,SAMHD1,SLFN11,SRGAP2,TBC1D12,TCP11L1,TRAM2

VSTM5,LINC00261,CEP85L,CACNA1H,CCL26,CD109,DAPK1,
DLK2,DUSP4,DZIP1L,FAM114A1,FAM167A,FAM46A,GRIP2,
HCN2,MIA3,PDE10A,RNF144B,RNF152,SMCHD1,STIM2
DOK5,FGF10,HSD17B6,KLHL41,KIAA0408,KLHL38,LONRF2,
MASP1,MOV10L1,MYOCD,NMNAT2,PALMD,PCDHGA5,PDE10A,
RASGRF2,RBMS1,SAMD4A,STXBP5L,SYDE2,SLC35G2,WWC2
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 PDE10A
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
DB00975phosphodiesterase 10AapprovedDipyridamole
DB01113phosphodiesterase 10AapprovedPapaverine
DB08383phosphodiesterase 10Aexperimental4,5-bis(4-methoxyphenyl)-2-thiophen-2-yl-1H-imidazole
DB08384phosphodiesterase 10Aexperimental2-({4-[4-(pyridin-4-ylmethyl)-1H-pyrazol-3-yl]phenoxy}methyl)quinoline
DB08386phosphodiesterase 10Aexperimental2-{[4-(4-pyridin-4-yl-1H-pyrazol-3-yl)phenoxy]methyl}quinoline
DB08387phosphodiesterase 10Aexperimental2-{[4-(1-methyl-4-pyridin-4-yl-1H-pyrazol-3-yl)phenoxy]methyl}quinoline
DB08389phosphodiesterase 10Aexperimental6,7-DIMETHOXY-4-[(3R)-3-(2-NAPHTHYLOXY)PYRROLIDIN-1-YL]QUINAZOLINE
DB08391phosphodiesterase 10Aexperimental6,7-DIMETHOXY-4-[(3R)-3-(QUINOXALIN-2-YLOXY)PYRROLIDIN-1-YL]QUINAZOLINE
DB08811phosphodiesterase 10AapprovedTofisopam
DB01151phosphodiesterase 10AapprovedDesipramine
DB00472phosphodiesterase 10AapprovedFluoxetine


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Cross referenced IDs for PDE10A
* 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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