|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PDE5A |
Basic gene info. | Gene symbol | PDE5A |
Gene name | phosphodiesterase 5A, cGMP-specific | |
Synonyms | CGB-PDE|CN5A|PDE5 | |
Cytomap | UCSC genome browser: 4q27 | |
Genomic location | chr4 :120415549-120549981 | |
Type of gene | protein-coding | |
RefGenes | NM_001083.3, NM_033430.2,NM_033437.3, | |
Ensembl id | ENSG00000138735 | |
Description | cGMP-binding cGMP-specific 3',5'-cyclic nucleotide phosphodiesterasecGMP-specific 3',5'-cyclic phosphodiesterasecGMP-specific phosphodiesterase PDE5A2cGMP-specific phosphodiesterase type 5Aphosphodiesterase isozyme 5 | |
Modification date | 20141207 | |
dbXrefs | MIM : 603310 | |
HGNC : HGNC | ||
Ensembl : ENSG00000138735 | ||
HPRD : 04497 | ||
Vega : OTTHUMG00000132971 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PDE5A | |
BioGPS: 8654 | ||
Gene Expression Atlas: ENSG00000138735 | ||
The Human Protein Atlas: ENSG00000138735 | ||
Pathway | NCI Pathway Interaction Database: PDE5A | |
KEGG: PDE5A | ||
REACTOME: PDE5A | ||
ConsensusPathDB | ||
Pathway Commons: PDE5A | ||
Metabolism | MetaCyc: PDE5A | |
HUMANCyc: PDE5A | ||
Regulation | Ensembl's Regulation: ENSG00000138735 | |
miRBase: chr4 :120,415,549-120,549,981 | ||
TargetScan: NM_001083 | ||
cisRED: ENSG00000138735 | ||
Context | iHOP: PDE5A | |
cancer metabolism search in PubMed: PDE5A | ||
UCL Cancer Institute: PDE5A | ||
Assigned class in ccmGDB | C |
Top |
Phenotypic Information for PDE5A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PDE5A |
Familial Cancer Database: PDE5A |
* This gene is included in those cancer gene databases. |
. | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: PDE5A |
MedGen: PDE5A (Human Medical Genetics with Condition) | |
ClinVar: PDE5A | |
Phenotype | MGI: PDE5A (International Mouse Phenotyping Consortium) |
PhenomicDB: PDE5A |
Mutations for PDE5A |
* 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 | PDE5A | chr4 | 120529791 | 120529811 | PDE5A | chr4 | 120529850 | 120529870 |
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 PDE5A 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 |
AW102720 | PDE5A | 10 | 163 | 4 | 120420968 | 120421121 | EHBP1 | 158 | 203 | 2 | 63251185 | 63251232 | |
CV345100 | LOC100131564 | 33 | 529 | 1 | 93801393 | 93801890 | PDE5A | 522 | 642 | 4 | 120436849 | 120436969 | |
BG996672 | PDE5A | 14 | 112 | 4 | 120471311 | 120471408 | ARGLU1 | 102 | 307 | 13 | 107196119 | 107196325 | |
BG980189 | CEACAM5 | 1 | 276 | 19 | 42212576 | 42260645 | PDE5A | 272 | 294 | 4 | 120432019 | 120432047 |
Other DBs for Structural Variants |
Top |
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 | 1 |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   | 1 | |||
GAIN (# sample) | 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) |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=60) | (# total SNVs=16) |
(# total SNVs=0) | (# total SNVs=2) |
Top |
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 |
chr4:120446754-120446754 | p.R577W | 3 |
chr4:120419875-120419875 | p.E837K | 2 |
chr4:120488258-120488258 | p.N291N | 2 |
chr4:120528376-120528376 | p.E77K | 2 |
chr4:120484024-120484024 | p.Q365H | 2 |
chr4:120528215-120528215 | p.K130N | 2 |
chr4:120463730-120463730 | p.R486* | 2 |
chr4:120446851-120446851 | p.? | 2 |
chr4:120428814-120428814 | p.T712P | 2 |
chr4:120463665-120463665 | p.Q507Q | 2 |
Top |
SNV Counts per Each Loci in TCGA data |
|
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 | 5 | 2 |   | 11 |   |   | 7 |   | 1 | 2 |   | 7 | 4 |   |   |   | 6 | 5 | 1 | 11 |
# mutation | 5 | 2 |   | 13 |   |   | 7 |   | 1 | 2 |   | 7 | 4 |   |   |   | 6 | 7 | 1 | 15 |
nonsynonymous SNV | 5 | 1 |   | 10 |   |   | 7 |   |   | 1 |   | 4 | 4 |   |   |   | 5 | 7 | 1 | 11 |
synonymous SNV |   | 1 |   | 3 |   |   |   |   | 1 | 1 |   | 3 |   |   |   |   | 1 |   |   | 4 |
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]) |
Top |
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 |
chr4:120446754 | p.R577W,PDE5A | 3 |
chr4:120427082 | p.R732Q,PDE5A | 2 |
chr4:120481508 | p.S381C,PDE5A | 2 |
chr4:120419875 | p.E837Q,PDE5A | 2 |
chr4:120484020 | p.F787C,PDE5A | 1 |
chr4:120422353 | p.L569M,PDE5A | 1 |
chr4:120432238 | p.N291N,PDE5A | 1 |
chr4:120527982 | p.E145K,PDE5A | 1 |
chr4:120463679 | p.F786L,PDE5A | 1 |
chr4:120528301 | p.F564C,PDE5A | 1 |
Other DBs for Point Mutations |
Copy Number for PDE5A 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] |
Top |
Gene Expression for PDE5A |
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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
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 |
AFP,ASH2L,BAG4,C16orf52,C8orf86,CACNG1,DDHD2, ERLIN2,HGSNAT,HTR7P1,KIAA1107,MOCS1,NTRK3,PDE5A, RAB11FIP1,RASSF6,SEMA5A,TAPT1,TBX3,TCEAL1,ULK2 | AEBP2,ARHGAP5,ATXN7,C7orf60,ISPD,LEMD3,MAP4K5, NUDT21,PDE5A,PLEKHA1,PPP1R12A,RSBN1,SCAMP1,SENP6, SOCS5,SORBS2,TRIM33,USP1,WASL,ZNF148,ZNF800 | ||||
ATP2B4,BVES,CAND2,CNTNAP1,FILIP1,GNAO1,KANK2, KCNMA1,KIAA2022,LRCH2,MAB21L2,MEIS1,MYLK,MYOCD, PDE5A,PDZRN4,PGR,PLN,PPP1R12B,RNF150,TMEM200B | ANKS1B,C20orf166-AS1,CAMK2G,CCBE1,DIXDC1,IL17RD,KCNMA1, LMO3,LMOD1,LOXL4,MEIS1,MEIS2,MRVI1,PDE5A, PGM5,PPP1R12A,RBFOX2,SCD5,SEMA3A,SEMA3C,TBC1D1 |
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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for PDE5A |
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 |
DB00203 | phosphodiesterase 5A, cGMP-specific | approved; investigational | Sildenafil | ||
DB00277 | phosphodiesterase 5A, cGMP-specific | approved | Theophylline | ||
DB00806 | phosphodiesterase 5A, cGMP-specific | approved; investigational | Pentoxifylline | ||
DB00820 | phosphodiesterase 5A, cGMP-specific | approved; investigational | Tadalafil | ||
DB00862 | phosphodiesterase 5A, cGMP-specific | approved | Vardenafil | ||
DB00975 | phosphodiesterase 5A, cGMP-specific | approved | Dipyridamole | ||
DB01972 | phosphodiesterase 5A, cGMP-specific | experimental | Guanosine-5'-Monophosphate | ||
DB03597 | phosphodiesterase 5A, cGMP-specific | experimental | Gamma-Glutamyl[S-(2-Iodobenzyl)Cysteinyl]Glycine | ||
DB04272 | phosphodiesterase 5A, cGMP-specific | experimental | Citric Acid | ||
DB06267 | phosphodiesterase 5A, cGMP-specific | approved; investigational | Udenafil | ||
DB07954 | phosphodiesterase 5A, cGMP-specific | experimental | 3-ISOBUTYL-1-METHYLXANTHINE | ||
DB08729 | phosphodiesterase 5A, cGMP-specific | experimental | 5-ethoxy-4-(1-methyl-7-oxo-3-propyl-6,7-dihydro-1H-pyrazolo[4,3-d]pyrimidin-5-yl)thiophene-2-sulfonamide | ||
DB01151 | phosphodiesterase 5A, cGMP-specific | approved | Desipramine | ||
DB00472 | phosphodiesterase 5A, cGMP-specific | approved | Fluoxetine |
Top |
Cross referenced IDs for PDE5A |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |