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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PDE4D |
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Phenotypic Information for PDE4D(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: PDE4D |
Familial Cancer Database: PDE4D |
* 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: PDE4D |
MedGen: PDE4D (Human Medical Genetics with Condition) | |
ClinVar: PDE4D | |
Phenotype | MGI: PDE4D (International Mouse Phenotyping Consortium) |
PhenomicDB: PDE4D |
Mutations for PDE4D |
* 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 |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
There's no intra-chromosomal structural variation. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
prostate | PDE4D | chr5 | 59621985 | 59623985 | NCOR2 | chr12 | 124837154 | 124839154 |
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 PDE4D 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 |
DA282561 | PDE4D | 1 | 100 | 5 | 59129537 | 59129636 | AGPAT4 | 101 | 575 | 6 | 161587303 | 161695030 | |
DB236218 | PDE4D | 1 | 210 | 5 | 59064071 | 59064280 | SLC16A9 | 208 | 580 | 10 | 61414072 | 61424081 | |
BE928480 | REPS1 | 68 | 299 | 6 | 139228509 | 139228740 | PDE4D | 299 | 325 | 5 | 59386751 | 59386781 | |
AW993560 | TAB2 | 8 | 160 | 6 | 149684678 | 149684831 | PDE4D | 146 | 342 | 5 | 58950802 | 58950999 | |
BI019872 | RAB37 | 14 | 226 | 17 | 72700776 | 72700988 | PDE4D | 219 | 373 | 5 | 58351301 | 58351453 | |
DA522054 | PDE4D | 1 | 267 | 5 | 58883684 | 58883950 | KCTD2 | 261 | 561 | 17 | 73059857 | 73060153 | |
BF367933 | PDE4D | 1 | 139 | 5 | 59495558 | 59495702 | PDE4D | 133 | 414 | 5 | 59495678 | 59495960 | |
DW442273 | PDE4D | 17 | 149 | 5 | 58676441 | 58676572 | PDE4D | 145 | 235 | 5 | 58677085 | 58677175 | |
BF917173 | PDE4D | 1 | 445 | 5 | 58445976 | 58446420 | KIAA1217 | 431 | 605 | 10 | 24835095 | 24835269 |
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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 |   |   |   |   |   |   |   |   | 1 |   | 2 |   |   |   |   |   |   | |||
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) |
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Stat. for Non-Synonymous SNVs (# total SNVs=52) | (# total SNVs=7) |
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(# total SNVs=2) | (# total SNVs=0) |
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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 |
chr5:58511596-58511596 | p.? | 3 |
chr5:58270597-58270597 | p.S639C | 2 |
chr5:58285638-58285638 | p.H330N | 2 |
chr5:58271593-58271593 | p.T499M | 2 |
chr5:58270587-58270587 | p.I642I | 1 |
chr5:58273028-58273028 | p.V430A | 1 |
chr5:58285753-58285754 | p.? | 1 |
chr5:58511763-58511763 | p.R27W | 1 |
chr5:58270781-58270781 | p.Q578* | 1 |
chr5:58289264-58289264 | p.T181N | 1 |
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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 | 2 | 6 |   | 10 |   |   | 6 |   | 2 |   |   | 7 | 5 | 1 |   |   | 10 | 3 |   | 10 |
# mutation | 2 | 6 |   | 10 |   |   | 6 |   | 2 |   |   | 7 | 5 | 1 |   |   | 10 | 3 |   | 14 |
nonsynonymous SNV | 2 | 6 |   | 9 |   |   | 5 |   | 1 |   |   | 5 | 2 | 1 |   |   | 8 | 1 |   | 10 |
synonymous SNV |   |   |   | 1 |   |   | 1 |   | 1 |   |   | 2 | 3 |   |   |   | 2 | 2 |   | 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]) |
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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 |
chr5:58271593 | p.R237Q,PDE4D | 2 |
chr5:58481063 | p.R44P | 2 |
chr5:59284456 | p.T411M,PDE4D | 2 |
chr5:58270597 | p.S75Y,PDE4D | 1 |
chr5:58289244 | p.A46A | 1 |
chr5:58511744 | p.C538C,PDE4D | 1 |
chr5:58271584 | p.E366K,PDE4D | 1 |
chr5:59189364 | p.L25L | 1 |
chr5:58273131 | p.E534K,PDE4D | 1 |
chr5:58270599 | p.V342V,PDE4D | 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 PDE4D |
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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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AVPI1,C19orf57,LINC00473,CXCL5,ECEL1,EYA4,FLJ45079, FYN,LOC441177,LSAMP,MAPK4,MCTP2,PDE3A,PDE4D, PLD1,PON1,PPARGC1A,PTP4A1,SLC7A5,SMOC1,SPINK6 | ACTC1,AGL,ART3,ASB2,ATP2A2,BVES,CTNNA3, DCAF6,DES,FLNC,FNDC5,KCNT1,LRRC2,MEF2C, NEXN,PDE4D,PHTF2,PLN,SGCA,SLC8A3,TMEM233 | ||||
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AKAP13,TMEM263,CRYBG3,ELL2,FAM114A1,IKZF2,IL6ST, KLF9,LHFPL2,MEF2A,PDE4B,PDE4D,PDE5A,PJA2, PLCL2,PPP1R12A,RAB27A,RAB8B,SGMS2,SNRK,TMTC2 | ABI2,AMIGO2,ARHGAP23,DCBLD2,DENND5A,ENAH,FAM124A, FAM129A,FGF12,HSPA2,MAP9,MASP1,MPDZ,MTMR9, MYOCD,PDE4D,PKD2,PRKAA2,SRF,VGLL3,WWC2 |
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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 PDE4D |
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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 |
DB00131 | phosphodiesterase 4D, cAMP-specific | approved; nutraceutical | Adenosine monophosphate | ![]() | ![]() |
DB00651 | phosphodiesterase 4D, cAMP-specific | approved | Dyphylline | ![]() | ![]() |
DB00920 | phosphodiesterase 4D, cAMP-specific | approved | Ketotifen | ![]() | ![]() |
DB01088 | phosphodiesterase 4D, cAMP-specific | approved; investigational | Iloprost | ![]() | ![]() |
DB01791 | phosphodiesterase 4D, cAMP-specific | experimental | Piclamilast | ![]() | ![]() |
DB01954 | phosphodiesterase 4D, cAMP-specific | experimental | 4-[3-(Cyclopentyloxy)-4-Methoxyphenyl]-2-Pyrrolidinone | ![]() | ![]() |
DB01959 | phosphodiesterase 4D, cAMP-specific | experimental | 3,5-Dimethyl-1-(3-Nitrophenyl)-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester | ![]() | ![]() |
DB02676 | phosphodiesterase 4D, cAMP-specific | experimental | 2-[3-(2-Hydroxy-1,1-Dihydroxymethyl-Ethylamino)-Propylamino]-2-Hydroxymethyl-Propane-1,3-Diol | ![]() | ![]() |
DB02918 | phosphodiesterase 4D, cAMP-specific | experimental | 6-(4-Difluoromethoxy-3-Methoxy-Phenyl)-2h-Pyridazin-3-One | ![]() | ![]() |
DB03183 | phosphodiesterase 4D, cAMP-specific | experimental | 1-(4-Aminophenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester | ![]() | ![]() |
DB03606 | phosphodiesterase 4D, cAMP-specific | experimental | (S)-Rolipram | ![]() | ![]() |
DB03849 | phosphodiesterase 4D, cAMP-specific | experimental | Cis-4-Cyano-4-[3-(Cyclopentyloxy)-4-Methoxyphenyl]Cyclohexanecarboxylic Acid | ![]() | ![]() |
DB04149 | phosphodiesterase 4D, cAMP-specific | experimental | (R)-Rolipram | ![]() | ![]() |
DB04271 | phosphodiesterase 4D, cAMP-specific | experimental | 3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester | ![]() | ![]() |
DB04469 | phosphodiesterase 4D, cAMP-specific | experimental | 1-(4-Methoxyphenyl)-3,5-Dimethyl-1h-Pyrazole-4-Carboxylic Acid Ethyl Ester | ![]() | ![]() |
DB05266 | phosphodiesterase 4D, cAMP-specific | approved; investigational | Ibudilast | ![]() | ![]() |
DB06842 | phosphodiesterase 4D, cAMP-specific | experimental | (4R)-4-(3-butoxy-4-methoxybenzyl)imidazolidin-2-one | ![]() | ![]() |
DB07051 | phosphodiesterase 4D, cAMP-specific | experimental | 3,5-DIMETHYL-1-PHENYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER | ![]() | ![]() |
DB07954 | phosphodiesterase 4D, cAMP-specific | experimental | 3-ISOBUTYL-1-METHYLXANTHINE | ![]() | ![]() |
DB08299 | phosphodiesterase 4D, cAMP-specific | experimental | 4-[8-(3-nitrophenyl)-1,7-naphthyridin-6-yl]benzoic acid | ![]() | ![]() |
DB01151 | phosphodiesterase 4D, cAMP-specific | approved | Desipramine | ![]() | ![]() |
DB00472 | phosphodiesterase 4D, cAMP-specific | approved | Fluoxetine | ![]() | ![]() |
DB00465 | phosphodiesterase 4D, cAMP-specific | approved | Ketorolac | ![]() | ![]() |
DB00533 | phosphodiesterase 4D, cAMP-specific | withdrawn; investigational | Rofecoxib | ![]() | ![]() |
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Cross referenced IDs for PDE4D |
* 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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