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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PDE3A |
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Phenotypic Information for PDE3A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PDE3A |
Familial Cancer Database: PDE3A |
* 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: PDE3A |
MedGen: PDE3A (Human Medical Genetics with Condition) | |
ClinVar: PDE3A | |
Phenotype | MGI: PDE3A (International Mouse Phenotyping Consortium) |
PhenomicDB: PDE3A |
Mutations for PDE3A |
* 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 |
breast | PDE3A | chr12 | 20725730 | 20725730 | PDE3A | chr12 | 20732634 | 20732634 |
ovary | PDE3A | chr12 | 20725383 | 20725403 | chr12 | 48697639 | 48697659 | |
ovary | PDE3A | chr12 | 20727870 | 20727890 | chr12 | 48699111 | 48699131 | |
ovary | PDE3A | chr12 | 20791784 | 20791804 | PDE3A | chr12 | 20717390 | 20717410 |
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 PDE3A 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 |
DA711191 | PDE3A | 1 | 402 | 12 | 20522829 | 20709645 | VGLL4 | 399 | 555 | 3 | 11606340 | 11606496 | |
BF755147 | PDE3A | 135 | 160 | 12 | 20749016 | 20749041 | RNF34 | 141 | 335 | 12 | 121838985 | 121839179 | |
AF118076 | PDE3A | 1 | 694 | 12 | 20597267 | 20597960 | CENPF | 693 | 2114 | 1 | 214822023 | 214827762 |
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 | 2 | 1 |   |   |   |   |   |   | 2 |   |   |   |   | 1 |   |   |   | |||
GAIN (# sample) | 2 | 1 |   |   |   |   |   |   | 2 |   |   |   |   | 1 |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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=133) | (# total SNVs=48) |
(# total SNVs=5) | (# total SNVs=2) |
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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 |
chr12:20766419-20766419 | p.E352K | 4 |
chr12:20522252-20522252 | p.D12N | 4 |
chr12:20766410-20766410 | p.V349I | 3 |
chr12:20806929-20806929 | p.R992C | 3 |
chr12:20522722-20522722 | p.C168C | 3 |
chr12:20523043-20523043 | p.L275L | 3 |
chr12:20769164-20769164 | p.R424C | 3 |
chr12:20522723-20522723 | p.E171fs*36 | 3 |
chr12:20790147-20790147 | p.R705S | 3 |
chr12:20807040-20807040 | p.D1029N | 2 |
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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 | 7 | 13 | 1 | 23 | 4 |   | 14 | 1 | 3 |   |   | 25 | 11 | 5 |   |   | 23 | 17 | 1 | 16 |
# mutation | 6 | 13 | 1 | 22 | 4 |   | 14 | 1 | 3 |   |   | 25 | 12 | 5 |   |   | 29 | 18 | 1 | 21 |
nonsynonymous SNV | 3 | 8 | 1 | 14 | 3 |   | 11 |   | 3 |   |   | 19 | 5 | 4 |   |   | 23 | 13 | 1 | 16 |
synonymous SNV | 3 | 5 |   | 8 | 1 |   | 3 | 1 |   |   |   | 6 | 7 | 1 |   |   | 6 | 5 |   | 5 |
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 |
chr12:20523043 | p.L275L | 5 |
chr12:20766410 | p.V27I,PDE3A | 3 |
chr12:20803400 | p.S530S,PDE3A | 2 |
chr12:20807040 | p.D609H,PDE3A | 2 |
chr12:20769164 | p.A220T | 2 |
chr12:20790115 | p.E30K,PDE3A | 2 |
chr12:20766419 | p.H32H,PDE3A | 2 |
chr12:20799828 | p.D95H,PDE3A | 2 |
chr12:20766427 | p.P373S,PDE3A | 2 |
chr12:20799875 | p.R102C,PDE3A | 2 |
Other DBs for Point Mutations |
Copy Number for PDE3A 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 PDE3A |
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 |
AVPI1,LINC00473,CALCA,ECEL1,FILIP1,GDF10,KSR1, LOC154822,LOC441177,MCF2,MCTP2,PDE3A,PDE4D,PLD1, PTP4A1,SGK1,SLC22A2,SLC7A5,SMOC1,UST,WNT1 | ABCA8,ABCC9,ADAMTSL3,ADIPOQ,ANO6,ARHGEF7,AVPR1A, VSTM4,C1QTNF7,CRYBG3,ESR2,TENM3___TENM1,PDE3A,PHLDB2, PREX2,PVRL3,SIK2,SLC16A7,SLC22A3,SOX5,TTLL7 | ||||
ADAM23,ENTPD5,FLVCR1,GAB1,HAVCR1,KCTD4,LGI4, LRFN2,LRRN2,MERTK,MYH2,OR6T1,PCDHA10,PDE3A, PTPRD,RAB9BP1,RASSF8,SLC30A1,SOX3,TBPL2,TNFAIP8L3 | SOGA1,DAAM1,FAM63B,GPR17,KLF7,NAV2,NKD1, PARD3B,PDE3A,PRDM11,PTPN13,PTPRM,RBMS3,ROR1, SCN3B,SNORD116-28,TACC1,TTBK2,WNT9A,ZC3H13,ZNF154 |
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 PDE3A |
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 |
DB00235 | phosphodiesterase 3A, cGMP-inhibited | approved | Milrinone | ||
DB00261 | phosphodiesterase 3A, cGMP-inhibited | approved | Anagrelide | ||
DB00277 | phosphodiesterase 3A, cGMP-inhibited | approved | Theophylline | ||
DB00922 | phosphodiesterase 3A, cGMP-inhibited | approved; investigational | Levosimendan | ||
DB01166 | phosphodiesterase 3A, cGMP-inhibited | approved | Cilostazol | ||
DB01223 | phosphodiesterase 3A, cGMP-inhibited | approved | Aminophylline | ||
DB01303 | phosphodiesterase 3A, cGMP-inhibited | approved | Oxtriphylline | ||
DB01427 | phosphodiesterase 3A, cGMP-inhibited | approved | Amrinone | ||
DB04880 | phosphodiesterase 3A, cGMP-inhibited | approved; investigational | Enoximone | ||
DB05266 | phosphodiesterase 3A, cGMP-inhibited | approved; investigational | Ibudilast | ||
DB08811 | phosphodiesterase 3A, cGMP-inhibited | approved | Tofisopam | ||
DB00131 | phosphodiesterase 3A, cGMP-inhibited | approved; nutraceutical | Adenosine monophosphate | ||
DB00125 | phosphodiesterase 3A, cGMP-inhibited | approved; nutraceutical | L-Arginine | ||
DB00155 | phosphodiesterase 3A, cGMP-inhibited | approved; nutraceutical | L-Citrulline | ||
DB00435 | phosphodiesterase 3A, cGMP-inhibited | approved | Nitric Oxide | ||
DB01151 | phosphodiesterase 3A, cGMP-inhibited | approved | Desipramine | ||
DB00472 | phosphodiesterase 3A, cGMP-inhibited | approved | Fluoxetine |
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Cross referenced IDs for PDE3A |
* 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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