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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PDE6A |
Basic gene info. | Gene symbol | PDE6A |
Gene name | phosphodiesterase 6A, cGMP-specific, rod, alpha | |
Synonyms | CGPR-A|PDEA|RP43 | |
Cytomap | UCSC genome browser: 5q31.2-q34 | |
Genomic location | chr5 :149237518-149324356 | |
Type of gene | protein-coding | |
RefGenes | NM_000440.2, | |
Ensembl id | ENSG00000132915 | |
Description | GMP-PDE alphaPDE V-B1cGMP phosphodiesterase alpha subunitrod cGMP-specific 3',5'-cyclic phosphodiesterase subunit alpharod photoreceptor cGMP phosphodiesterase alpha subunit | |
Modification date | 20141219 | |
dbXrefs | MIM : 180071 | |
HGNC : HGNC | ||
Ensembl : ENSG00000132915 | ||
HPRD : 01570 | ||
Vega : OTTHUMG00000130047 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PDE6A | |
BioGPS: 5145 | ||
Gene Expression Atlas: ENSG00000132915 | ||
The Human Protein Atlas: ENSG00000132915 | ||
Pathway | NCI Pathway Interaction Database: PDE6A | |
KEGG: PDE6A | ||
REACTOME: PDE6A | ||
ConsensusPathDB | ||
Pathway Commons: PDE6A | ||
Metabolism | MetaCyc: PDE6A | |
HUMANCyc: PDE6A | ||
Regulation | Ensembl's Regulation: ENSG00000132915 | |
miRBase: chr5 :149,237,518-149,324,356 | ||
TargetScan: NM_000440 | ||
cisRED: ENSG00000132915 | ||
Context | iHOP: PDE6A | |
cancer metabolism search in PubMed: PDE6A | ||
UCL Cancer Institute: PDE6A | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PDE6A(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PDE6A |
Familial Cancer Database: PDE6A |
* 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: PDE6A |
MedGen: PDE6A (Human Medical Genetics with Condition) | |
ClinVar: PDE6A | |
Phenotype | MGI: PDE6A (International Mouse Phenotyping Consortium) |
PhenomicDB: PDE6A |
Mutations for PDE6A |
* 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 | PDE6A | chr5 | 149241504 | 149241524 | MIR143HG | chr5 | 148811239 | 148811259 |
ovary | PDE6A | chr5 | 149276141 | 149276161 | CSNK1A1 | chr5 | 148912648 | 148912668 |
ovary | PDE6A | chr5 | 149279921 | 149279941 | ABLIM3 | chr5 | 148582671 | 148582691 |
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 PDE6A 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 |
BQ638079 | PDE6A | 237 | 340 | 5 | 149284906 | 149285009 | PDE6A | 336 | 597 | 5 | 149285025 | 149285286 |
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 |   |   |   |   |   |   |   |   |   |   | 1 |   |   | 1 |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   | 1 |   |   | 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=70) | (# total SNVs=19) |
(# total SNVs=3) | (# total SNVs=1) |
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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 |
chr5:149294570-149294570 | p.E312K | 4 |
chr5:149313501-149313501 | p.R237C | 3 |
chr5:149276332-149276332 | p.R472T | 2 |
chr5:149242808-149242808 | p.E794K | 2 |
chr5:149240474-149240474 | p.S856C | 2 |
chr5:149278968-149278968 | p.P411P | 2 |
chr5:149240510-149240510 | p.G844fs*>17 | 2 |
chr5:149323922-149323922 | p.I105I | 2 |
chr5:149278060-149278060 | p.Q425* | 2 |
chr5:149278947-149278947 | p.T418T | 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 | 1 | 3 |   | 10 | 2 |   | 1 |   | 1 |   | 1 | 13 | 4 | 3 |   | 1 | 13 | 11 |   | 11 |
# mutation | 1 | 3 |   | 11 | 2 |   | 1 |   | 1 |   | 1 | 13 | 4 | 3 |   | 1 | 19 | 11 |   | 12 |
nonsynonymous SNV | 1 | 1 |   | 10 | 2 |   | 1 |   | 1 |   |   | 9 | 4 | 3 |   |   | 12 | 6 |   | 9 |
synonymous SNV |   | 2 |   | 2 |   |   |   |   |   |   | 1 | 4 |   |   |   | 1 | 7 | 5 |   | 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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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 |
chr5:149240474 | p.S856Y | 2 |
chr5:149323840 | p.V133I | 2 |
chr5:149313501 | p.R237C | 2 |
chr5:149313514 | p.N232N | 2 |
chr5:149264407 | p.E327E | 1 |
chr5:149310672 | p.A194T | 1 |
chr5:149276035 | p.L36F | 1 |
chr5:149314188 | p.E709K | 1 |
chr5:149324052 | p.F508F | 1 |
chr5:149247336 | p.H324H | 1 |
Other DBs for Point Mutations |
Copy Number for PDE6A 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 PDE6A |
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 |
AQP2,PRR26,GFRA3,GRK1,GRXCR1,LOC157381,LOC339788, LOXHD1,NOBOX,NT5C1B,PDE6A,POM121L8P,POU5F1B,PRAMEF5, PRAMEF9,SIM1,TPD52L3,TRIM53AP,TSGA10IP,UBE2U,ZAR1L | AQP2,VRTN,C1orf95,TEX37,C2orf71,CC2D2A,CPNE6, GFRA3,LOC153910,MAS1,MMD2,OR1M1,PDE6A,PMP2, POU4F1,POU5F1B,SHC3,SLC26A2,SLCO6A1,TBX18,TEX15 | ||||
ABCC13,B4GALNT2,CD24,CEACAM7,FABP1,TMEM236,NXPE4, RMDN2,FRYL,GLYATL2,OR13C4,PBLD,PDE6A,RB1CC1, SATB2,SLC26A2,SLC26A3,SLC4A10,SLC5A8,TMEM72,TRPM6 | AGFG2,AHCYL2,AMACR,APOBEC3B,AQP8,FBXO34,LGALS4, MKRN1,MTMR11,PDE6A,PDE8A,PLCD3,PPARG,PRR15, SELENBP1,SFXN5,SGK2,SH3BGRL2,SLC26A2,SLC45A2,ZBTB7C |
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 PDE6A |
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 |
DB00472 | phosphodiesterase 6A, cGMP-specific, rod, alpha | approved | Fluoxetine |
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Cross referenced IDs for PDE6A |
* 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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