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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PDE4B |
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Phenotypic Information for PDE4B(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PDE4B |
Familial Cancer Database: PDE4B |
* 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 | 600127; gene. |
Orphanet | |
Disease | KEGG Disease: PDE4B |
MedGen: PDE4B (Human Medical Genetics with Condition) | |
ClinVar: PDE4B | |
Phenotype | MGI: PDE4B (International Mouse Phenotyping Consortium) |
PhenomicDB: PDE4B |
Mutations for PDE4B |
* 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 | PDE4B | chr1 | 66817085 | 66817085 | PDE4B | chr1 | 66837389 | 66837389 |
breast | PDE4B | chr1 | 66838567 | 66838567 | chr1 | 66874083 | 66874083 |
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 PDE4B 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 |
BQ352220 | NDUFS3 | 14 | 150 | 11 | 47603938 | 47605919 | PDE4B | 139 | 319 | 1 | 66838835 | 66839015 | |
L20971 | PDE4B | 6 | 389 | 1 | 66839227 | 66839611 | PDE4B | 380 | 4051 | 1 | 66797687 | 66839942 | |
AA226609 | PDE4B | 6 | 86 | 1 | 66838960 | 66839041 | PDE4B | 82 | 177 | 1 | 66838958 | 66839057 | |
BF359219 | S100A16 | 1 | 192 | 1 | 153579953 | 153580145 | PDE4B | 184 | 245 | 1 | 66836309 | 66836370 |
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 | 3 | 1 |   |   |   |   |   |   | 2 |   |   |   |   |   |   |   |   | |||
GAIN (# sample) | 2 | 1 |   |   |   |   |   |   | 2 |   |   |   |   |   |   |   |   | |||
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=77) | (# total SNVs=24) |
(# total SNVs=1) | (# 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 |
chr1:66833737-66833737 | p.D551N | 3 |
chr1:66828886-66828886 | p.I352I | 2 |
chr1:66384329-66384329 | p.S31F | 2 |
chr1:66379023-66379023 | p.T9M | 2 |
chr1:66384348-66384348 | p.I37I | 2 |
chr1:66713153-66713153 | p.E98* | 2 |
chr1:66833528-66833528 | p.D512N | 2 |
chr1:66821257-66821257 | p.S265R | 2 |
chr1:66821258-66821258 | p.R266R | 2 |
chr1:66829101-66829101 | p.L377L | 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 | 5 | 3 | 15 | 1 |   | 7 |   | 1 |   |   | 11 | 3 | 2 |   |   | 11 | 10 |   | 13 |
# mutation | 1 | 5 | 3 | 15 | 1 |   | 7 |   | 1 |   |   | 11 | 3 | 2 |   |   | 10 | 10 |   | 15 |
nonsynonymous SNV | 1 | 4 | 2 | 10 | 1 |   | 4 |   | 1 |   |   | 8 | 3 | 1 |   |   | 7 | 6 |   | 10 |
synonymous SNV |   | 1 | 1 | 5 |   |   | 3 |   |   |   |   | 3 |   | 1 |   |   | 3 | 4 |   | 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 |
chr1:66384348 | p.S245L,PDE4B | 3 |
chr1:66829220 | p.I37I,PDE4B | 3 |
chr1:66833737 | p.D379N,PDE4B | 2 |
chr1:66829176 | p.D126Y,PDE4B | 2 |
chr1:66829177 | p.I180I,PDE4B | 2 |
chr1:66713282 | p.G146S,PDE4B | 2 |
chr1:66723334 | p.D230D,PDE4B | 2 |
chr1:66828886 | p.V231M,PDE4B | 2 |
chr1:66379018 | p.V7V,PDE4B | 1 |
chr1:66798171 | p.P40P | 1 |
Other DBs for Point Mutations |
Copy Number for PDE4B 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 PDE4B |
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 |
MB21D1,CFLAR,DOCK7,CCDC71L,FUT4,MPZL1,NCK1, NCOA7,NFIL3,OSMR,PDE4B,PLD1,PNRC1,PSME4, RAB29,RNF145,SLC5A6,SOD2,SOX9,TMEM123,VASH2 | ANK3,ATL2,CHAF1B,DYRK1A,FAM160A1,FBXO34,ITGB6, NAA15,NT5C2,PDE4B,PDE7A,PM20D2,PSME4,PSTPIP2, RPAP3,SACS,SOCS6,SRPK1,TEX10,THAP9,TIAM2 | ||||
ARHGAP20,ARHGAP24,ARHGAP31,CASS4,CYTIP,ETS1,FMNL1, ITM2A,LCP2,NLRP3,PDE4B,PDE4D,PRKCH,RAB27A, RAB8B,SAMSN1,SCARF1,SRGN,STK10,TOX,TRAM2 | AREG,ARL4C,CD80,CHST2,CTLA4,CXCL1,CXCL2, CXCL3,DEFB103B,IL1B,MMP12,NFKBIZ,PDE4B,PFKFB3, PIM3,PLAU,PRSS27,STX11,WFDC12,YRDC,ZC3H12A |
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 PDE4B |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Chemistry | BindingDB | Q07343; -. |
Chemistry | ChEMBL | CHEMBL2111340; -. |
Chemistry | GuidetoPHARMACOLOGY | 1301; -. |
Organism-specific databases | PharmGKB | PA33129; -. |
Organism-specific databases | CTD | 5142; -. |
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 |
DB00131 | phosphodiesterase 4B, cAMP-specific | approved; nutraceutical | Adenosine monophosphate | ||
DB00201 | phosphodiesterase 4B, cAMP-specific | approved | Caffeine | ||
DB00277 | phosphodiesterase 4B, cAMP-specific | approved | Theophylline | ||
DB00651 | phosphodiesterase 4B, cAMP-specific | approved | Dyphylline | ||
DB00806 | phosphodiesterase 4B, cAMP-specific | approved; investigational | Pentoxifylline | ||
DB00824 | phosphodiesterase 4B, cAMP-specific | approved | Enprofylline | ||
DB00920 | phosphodiesterase 4B, cAMP-specific | approved | Ketotifen | ||
DB01088 | phosphodiesterase 4B, cAMP-specific | approved; investigational | Iloprost | ||
DB01113 | phosphodiesterase 4B, cAMP-specific | approved | Papaverine | ||
DB01412 | phosphodiesterase 4B, cAMP-specific | approved | Theobromine | ||
DB01427 | phosphodiesterase 4B, cAMP-specific | approved | Amrinone | ||
DB01647 | phosphodiesterase 4B, cAMP-specific | experimental | (R)-Mesopram | ||
DB01791 | phosphodiesterase 4B, cAMP-specific | experimental | Piclamilast | ||
DB01954 | phosphodiesterase 4B, cAMP-specific | experimental | 4-[3-(Cyclopentyloxy)-4-Methoxyphenyl]-2-Pyrrolidinone | ||
DB01959 | phosphodiesterase 4B, cAMP-specific | experimental | 3,5-Dimethyl-1-(3-Nitrophenyl)-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester | ||
DB02660 | phosphodiesterase 4B, cAMP-specific | experimental | Filaminast | ||
DB03349 | phosphodiesterase 4B, cAMP-specific | experimental | 8-Bromo-Adenosine-5'-Monophosphate | ||
DB03606 | phosphodiesterase 4B, cAMP-specific | experimental | (S)-Rolipram | ||
DB03807 | phosphodiesterase 4B, cAMP-specific | experimental | 1-(2-Chlorophenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester | ||
DB03849 | phosphodiesterase 4B, cAMP-specific | experimental | Cis-4-Cyano-4-[3-(Cyclopentyloxy)-4-Methoxyphenyl]Cyclohexanecarboxylic Acid | ||
DB04149 | phosphodiesterase 4B, cAMP-specific | experimental | (R)-Rolipram | ||
DB04530 | phosphodiesterase 4B, cAMP-specific | experimental | S,S-(2-Hydroxyethyl)Thiocysteine | ||
DB05266 | phosphodiesterase 4B, cAMP-specific | approved; investigational | Ibudilast | ||
DB06909 | phosphodiesterase 4B, cAMP-specific | experimental | 1-ethyl-N-(phenylmethyl)-4-(tetrahydro-2H-pyran-4-ylamino)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide | ||
DB08299 | phosphodiesterase 4B, cAMP-specific | experimental | 4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid | ||
DB01151 | phosphodiesterase 4B, cAMP-specific | approved | Desipramine | ||
DB00472 | phosphodiesterase 4B, cAMP-specific | approved | Fluoxetine |
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Cross referenced IDs for PDE4B |
* 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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