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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PDE8B |
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Phenotypic Information for PDE8B(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PDE8B |
Familial Cancer Database: PDE8B |
* 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/ |
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KEGG_PURINE_METABOLISM |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: PDE8B |
MedGen: PDE8B (Human Medical Genetics with Condition) | |
ClinVar: PDE8B | |
Phenotype | MGI: PDE8B (International Mouse Phenotyping Consortium) |
PhenomicDB: PDE8B |
Mutations for PDE8B |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'. |
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- 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'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
breast | PDE8B | chr5 | 76513508 | 76513508 | PDE8B | chr5 | 76722336 | 76722336 |
breast | PDE8B | chr5 | 76722208 | 76722208 | GMDS | chr6 | 2163549 | 2163549 |
ovary | PDE8B | chr5 | 76521295 | 76521315 | PDE8B | chr5 | 76508727 | 76508747 |
ovary | PDE8B | chr5 | 76646625 | 76646645 | PDE8B | chr5 | 76513562 | 76513582 |
pancreas | PDE8B | chr5 | 76691122 | 76691322 | ZNF286A | chr17 | 15610430 | 15610630 |
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) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PDE8B 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 |
M85313 | PDE8B | 1 | 184 | 5 | 76523256 | 76523439 | TERF2IP | 173 | 412 | 16 | 75690999 | 75691242 |
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Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   | 5 |   |   |   | 1 |   |   |   |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   | 5 |   |   |   | 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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Stat. for Non-Synonymous SNVs (# total SNVs=78) | (# total SNVs=26) |
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(# total SNVs=1) | (# total SNVs=1) |
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* 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 |
chr5:76703223-76703223 | p.R436C | 4 |
chr5:76700600-76700600 | p.S422S | 2 |
chr5:76714204-76714204 | p.H688Y | 2 |
chr5:76646938-76646938 | p.Q356K | 2 |
chr5:76709015-76709015 | p.R598W | 2 |
chr5:76646899-76646899 | p.G343R | 2 |
chr5:76624876-76624876 | p.S215L | 2 |
chr5:76717755-76717755 | p.R787H | 2 |
chr5:76715631-76715631 | p.M723I | 2 |
chr5:76621417-76621417 | p.A151A | 2 |
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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 |   | 15 | 2 |   | 7 | 1 | 1 |   |   | 11 | 4 | 2 | 1 | 1 | 23 | 6 |   | 17 |
# mutation |   | 1 |   | 17 | 2 |   | 7 | 1 | 1 |   |   | 11 | 4 | 2 | 1 | 1 | 24 | 6 |   | 20 |
nonsynonymous SNV |   |   |   | 13 | 1 |   | 5 |   | 1 |   |   | 6 | 2 |   |   | 1 | 19 | 5 |   | 19 |
synonymous SNV |   | 1 |   | 4 | 1 |   | 2 | 1 |   |   |   | 5 | 2 | 2 | 1 |   | 5 | 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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* 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 |
chr5:76714063 | p.R501W,PDE8B | 2 |
chr5:76700600 | p.S325S,PDE8B | 2 |
chr5:76703223 | p.R339C,PDE8B | 2 |
chr5:76709015 | p.S195L,PDE8B | 2 |
chr5:76624876 | p.D544N,PDE8B | 2 |
chr5:76645327 | p.R304W,PDE8B | 1 |
chr5:76621379 | p.G421R,PDE8B | 1 |
chr5:76700558 | p.L546S,PDE8B | 1 |
chr5:76715650 | p.T710P,PDE8B | 1 |
chr5:76624826 | p.S123S,PDE8B | 1 |
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* 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. |
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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 PDE8B |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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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BBX,LINC00473,ECEL1,EDARADD,ERBB2IP,ERO1LB,EVX1, FKTN,GABRR3,HSDL2,MCTP2,MTUS1,PDE4D,PDE8B, PITX1,PROKR2,SLC6A14,SMAD5,SRFBP1,WDR41,ZBED3 | ACO1,AOC3,ASPH,ATP2B4,NPR3,CPED1,CCDC3, COBLL1,ESYT1,FZD5,MDFIC,MYO1C,PALM2-AKAP2,PARVA, PDE8B,PLIN1,PLXNA4,PRKAR2B,PYGL,SLC25A16,VKORC1L1 | ||||
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BPIFB3,NAT16,DCHS2,DDHD1,FAM184A,FMNL3,GPM6B, GREB1,HIP1,ITPR1,TP73-AS1,KRTAP10-11,LOC100272216,MCTP1, MPP2,NPTXR,PDE8B,PPM1K,TXLNB,ZNF483,ZNF671 | ASIC1,ATP1A2,C20orf166-AS1,NPR3,FAXDC2,CAMK2G,PIEZO2, FBXL22,RBFOX3,LOC92249,LOXL4,MEIS2,NRK,NRXN2, PDE2A,PDE8B,PLCD4,RGAG4,SLC29A1,SOX11,SRPK3 |
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* 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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Pharmacological Information for PDE8B |
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DB Category | DB Name | DB's ID and Url link |
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* Gene Centered Interaction Network. |
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* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00920 | phosphodiesterase 8B | approved | Ketotifen | ![]() | ![]() |
DB00472 | phosphodiesterase 8B | approved | Fluoxetine | ![]() | ![]() |
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Cross referenced IDs for PDE8B |
* 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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