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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PDE7A |
Basic gene info. | Gene symbol | PDE7A |
Gene name | phosphodiesterase 7A | |
Synonyms | HCP1|PDE7 | |
Cytomap | UCSC genome browser: 8q13 | |
Genomic location | chr8 :66626568-66753969 | |
Type of gene | protein-coding | |
RefGenes | NM_001242318.2, NM_002603.3,NM_002604.2, | |
Ensembl id | ENSG00000205268 | |
Description | TM22high affinity cAMP-specific 3',5'-cyclic phosphodiesterase 7Aphosphodiesterase isozyme 7 | |
Modification date | 20141207 | |
dbXrefs | MIM : 171885 | |
HGNC : HGNC | ||
HPRD : 01386 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PDE7A | |
BioGPS: 5150 | ||
Gene Expression Atlas: ENSG00000205268 | ||
The Human Protein Atlas: ENSG00000205268 | ||
Pathway | NCI Pathway Interaction Database: PDE7A | |
KEGG: PDE7A | ||
REACTOME: PDE7A | ||
ConsensusPathDB | ||
Pathway Commons: PDE7A | ||
Metabolism | MetaCyc: PDE7A | |
HUMANCyc: PDE7A | ||
Regulation | Ensembl's Regulation: ENSG00000205268 | |
miRBase: chr8 :66,626,568-66,753,969 | ||
TargetScan: NM_001242318 | ||
cisRED: ENSG00000205268 | ||
Context | iHOP: PDE7A | |
cancer metabolism search in PubMed: PDE7A | ||
UCL Cancer Institute: PDE7A | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PDE7A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PDE7A |
Familial Cancer Database: PDE7A |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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: PDE7A |
MedGen: PDE7A (Human Medical Genetics with Condition) | |
ClinVar: PDE7A | |
Phenotype | MGI: PDE7A (International Mouse Phenotyping Consortium) |
PhenomicDB: PDE7A |
Mutations for PDE7A |
* 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 | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | PDE7A | chr8 | 66654870 | 66654890 | PDE7A | chr8 | 66655113 | 66655133 |
pancreas | PDE7A | chr8 | 66748009 | 66748029 | PDE7A | chr8 | 66748786 | 66748806 |
pancreas | PDE7A | chr8 | 66749842 | 66749862 | chr8 | 66754769 | 66754789 |
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 PDE7A related fusion information. |
ID | 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 |
BM722198 | PDE7A | 1 | 301 | 8 | 66680775 | 66681075 | PDE7A | 301 | 509 | 8 | 66682357 | 66682565 |
Other DBs for Structural Variants |
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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 | 4 |   | 1 |   |   |   |   |   |   |   | 1 |   |   |   |   |   | 1 | |||
GAIN (# sample) | 4 |   |   |   |   |   |   |   |   |   | 1 |   |   |   |   |   | 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=32) | (# total SNVs=10) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr8:66635851-66635851 | p.I364V | 10 |
chr8:66639512-66639512 | p.D215N | 2 |
chr8:66631619-66631619 | p.K426T | 2 |
chr8:66631704-66631704 | p.L398L | 2 |
chr8:66635769-66635769 | p.? | 2 |
chr8:66635801-66635801 | p.T380T | 2 |
chr8:66631579-66631579 | p.D439D | 2 |
chr8:66631607-66631607 | p.R430I | 1 |
chr8:66659976-66659976 | p.R90* | 1 |
chr8:66637113-66637113 | p.D296N | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   | 9 |   |   | 3 |   |   |   |   | 3 |   | 1 |   |   | 2 | 5 | 1 | 2 |
# mutation | 1 |   |   | 9 |   |   | 3 |   |   |   |   | 3 |   | 1 |   |   | 2 | 5 | 1 | 2 |
nonsynonymous SNV | 1 |   |   | 7 |   |   | 3 |   |   |   |   | 3 |   | 1 |   |   | 2 | 4 |   | 1 |
synonymous SNV |   |   |   | 2 |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 | 1 | 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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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 |
chr8:66637059 | p.G340C,PDE7A | 2 |
chr8:66635829 | p.A320A,PDE7A | 1 |
chr8:66651787 | p.L35V | 1 |
chr8:66636582 | p.T312I,PDE7A | 1 |
chr8:66659908 | p.S31C | 1 |
chr8:66659966 | p.L302L,PDE7A | 1 |
chr8:66637117 | p.F299L,PDE7A | 1 |
chr8:66691967 | p.V280A,PDE7A | 1 |
chr8:66637142 | p.T278I,PDE7A | 1 |
chr8:66691976 | p.H216H,PDE7A | 1 |
Other DBs for Point Mutations |
Copy Number for PDE7A 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 PDE7A |
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. |
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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 |
BCL11A,CDCA7,CDCA8,CENPA,AMER1,FAM171A1,KDM2B, LBR,MEX3A,NDC80,PDE7A,PTDSS1,RAD51AP1,SLCO5A1, STMN1,SUV39H2,TAF5,TEX10,TTK,TTLL4,ZNF695 | ATL2,KANSL2,DIEXF,CCL28,ELF5,ETV6,KIT, KLF5,LARS,METAP1,NKRF,NT5C2,PDE7A,PM20D2, PSTPIP2,RAVER2,TCERG1,TEX10,TIGD1,TIGD2,ZNF485 | ||||
ARFGEF1,CHD7,CSPP1,E2F5,KHDRBS3,LAPTM4B,LRRC14, MTBP,NSMAF,OSGIN2,PABPC1,PDE7A,PTDSS1,SLC25A32, SUZ12P1,VCPIP1,ZNF251,ZNF623,ZNF696,ZNF707,ZNF7 | BEND4,CARD11,ETS1,GVINP1,IKZF1,IKZF3,JAK3, MAP4K1,NLRC3,NUP210,P2RX5,P2RY8,PASK,PDCD1, PDE7A,POU2AF1,RLTPR,SP140,STAP1,TMC8,ZNF831 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for PDE7A |
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 7A | approved | Dyphylline | ||
DB00920 | phosphodiesterase 7A | approved | Ketotifen | ||
DB07954 | phosphodiesterase 7A | experimental | 3-ISOBUTYL-1-METHYLXANTHINE | ||
DB08602 | phosphodiesterase 7A | experimental | 3-(2,6-difluorophenyl)-2-(methylthio)quinazolin-4(3H)-one | ||
DB01151 | phosphodiesterase 7A | approved | Desipramine | ||
DB00472 | phosphodiesterase 7A | approved | Fluoxetine |
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Cross referenced IDs for PDE7A |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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