Browse PDE6B

Summary
SymbolPDE6B
Namephosphodiesterase 6B, cGMP-specific, rod, beta
Aliases CSNB3; rd1; RP40; CSNBAD2; congenital stationary night blindness 3, autosomal dominant; PDEB; GMP-PDE beta; ......
Chromosomal Location4p16.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Membrane; Lipid-anchor.
Domain PF01590 GAF domain
PF00233 3'5'-cyclic nucleotide phosphodiesterase
Function

This protein participates in processes of transmission and amplification of the visual signal. Necessary for the formation of a functional phosphodiesterase holoenzyme.

> Gene Ontology
 
Biological Process GO:0001654 eye development
GO:0006874 cellular calcium ion homeostasis
GO:0006875 cellular metal ion homeostasis
GO:0007223 Wnt signaling pathway, calcium modulating pathway
GO:0007423 sensory organ development
GO:0007601 visual perception
GO:0007602 phototransduction
GO:0007603 phototransduction, visible light
GO:0008277 regulation of G-protein coupled receptor protein signaling pathway
GO:0009116 nucleoside metabolic process
GO:0009119 ribonucleoside metabolic process
GO:0009123 nucleoside monophosphate metabolic process
GO:0009126 purine nucleoside monophosphate metabolic process
GO:0009150 purine ribonucleotide metabolic process
GO:0009161 ribonucleoside monophosphate metabolic process
GO:0009167 purine ribonucleoside monophosphate metabolic process
GO:0009314 response to radiation
GO:0009416 response to light stimulus
GO:0009581 detection of external stimulus
GO:0009582 detection of abiotic stimulus
GO:0009583 detection of light stimulus
GO:0009584 detection of visible light
GO:0016055 Wnt signaling pathway
GO:0016056 rhodopsin mediated signaling pathway
GO:0022400 regulation of rhodopsin mediated signaling pathway
GO:0035567 non-canonical Wnt signaling pathway
GO:0042278 purine nucleoside metabolic process
GO:0043010 camera-type eye development
GO:0046037 GMP metabolic process
GO:0046128 purine ribonucleoside metabolic process
GO:0050953 sensory perception of light stimulus
GO:0051480 regulation of cytosolic calcium ion concentration
GO:0055074 calcium ion homeostasis
GO:0060041 retina development in camera-type eye
GO:0071214 cellular response to abiotic stimulus
GO:0071478 cellular response to radiation
GO:0071482 cellular response to light stimulus
GO:0072503 cellular divalent inorganic cation homeostasis
GO:0072507 divalent inorganic cation homeostasis
GO:0198738 cell-cell signaling by wnt
GO:1901068 guanosine-containing compound metabolic process
GO:1901657 glycosyl compound metabolic process
Molecular Function GO:0004112 cyclic-nucleotide phosphodiesterase activity
GO:0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
GO:0008081 phosphoric diester hydrolase activity
GO:0042578 phosphoric ester hydrolase activity
GO:0047555 3',5'-cyclic-GMP phosphodiesterase activity
Cellular Component GO:0001750 photoreceptor outer segment
GO:0005929 cilium
GO:0031253 cell projection membrane
GO:0031513 nonmotile primary cilium
GO:0044441 ciliary part
GO:0060170 ciliary membrane
GO:0072372 primary cilium
GO:0097381 photoreceptor disc membrane
> KEGG and Reactome Pathway
 
KEGG hsa04744 Phototransduction
hsa00230 Purine metabolism
Reactome R-HSA-2485179: Activation of the phototransduction cascade
R-HSA-3858494: Beta-catenin independent WNT signaling
R-HSA-4086398: Ca2+ pathway
R-HSA-2514859: Inactivation, recovery and regulation of the phototransduction cascade
R-HSA-162582: Signal Transduction
R-HSA-195721: Signaling by Wnt
R-HSA-2514856: The phototransduction cascade
R-HSA-2187338: Visual phototransduction
Summary
SymbolPDE6B
Namephosphodiesterase 6B, cGMP-specific, rod, beta
Aliases CSNB3; rd1; RP40; CSNBAD2; congenital stationary night blindness 3, autosomal dominant; PDEB; GMP-PDE beta; ......
Chromosomal Location4p16.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between PDE6B and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 

There is no record.
Summary
SymbolPDE6B
Namephosphodiesterase 6B, cGMP-specific, rod, beta
Aliases CSNB3; rd1; RP40; CSNBAD2; congenital stationary night blindness 3, autosomal dominant; PDEB; GMP-PDE beta; ......
Chromosomal Location4p16.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of PDE6B in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NSNA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NSNA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NSNA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NSNA/NS
24476824shRNAmelanomaB16Primary screen NA/NSNA/NS
24476824shRNAmelanomaB16Secondary screen NA/NSNA/NS
Summary
SymbolPDE6B
Namephosphodiesterase 6B, cGMP-specific, rod, beta
Aliases CSNB3; rd1; RP40; CSNBAD2; congenital stationary night blindness 3, autosomal dominant; PDEB; GMP-PDE beta; ......
Chromosomal Location4p16.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of PDE6B in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.0510.84
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.2360.588
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.270.467
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160.260.522
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-0.0690.95
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.6850.657
729033130MelanomaallAnti-PD-1 (nivolumab) 2623-0.0870.829
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.740.278
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 1112-0.9830.169
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.8550.482
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.4860.794
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.2570.19
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of PDE6B in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 277314.81.413.40.0181
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 275914.81.713.10.032
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21179.509.50.492
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)86250250.473
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13110001
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 91611.16.24.91
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 592011.18.91
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 382710.53.76.80.393
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 221313.67.75.91
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16146.206.21
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolPDE6B
Namephosphodiesterase 6B, cGMP-specific, rod, beta
Aliases CSNB3; rd1; RP40; CSNBAD2; congenital stationary night blindness 3, autosomal dominant; PDEB; GMP-PDE beta; ......
Chromosomal Location4p16.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of PDE6B. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolPDE6B
Namephosphodiesterase 6B, cGMP-specific, rod, beta
Aliases CSNB3; rd1; RP40; CSNBAD2; congenital stationary night blindness 3, autosomal dominant; PDEB; GMP-PDE beta; ......
Chromosomal Location4p16.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of PDE6B. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by PDE6B.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolPDE6B
Namephosphodiesterase 6B, cGMP-specific, rod, beta
Aliases CSNB3; rd1; RP40; CSNBAD2; congenital stationary night blindness 3, autosomal dominant; PDEB; GMP-PDE beta; ......
Chromosomal Location4p16.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of PDE6B. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolPDE6B
Namephosphodiesterase 6B, cGMP-specific, rod, beta
Aliases CSNB3; rd1; RP40; CSNBAD2; congenital stationary night blindness 3, autosomal dominant; PDEB; GMP-PDE beta; ......
Chromosomal Location4p16.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of PDE6B expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolPDE6B
Namephosphodiesterase 6B, cGMP-specific, rod, beta
Aliases CSNB3; rd1; RP40; CSNBAD2; congenital stationary night blindness 3, autosomal dominant; PDEB; GMP-PDE beta; ......
Chromosomal Location4p16.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between PDE6B and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolPDE6B
Namephosphodiesterase 6B, cGMP-specific, rod, beta
Aliases CSNB3; rd1; RP40; CSNBAD2; congenital stationary night blindness 3, autosomal dominant; PDEB; GMP-PDE beta; ......
Chromosomal Location4p16.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting PDE6B collected from DrugBank database.
> Drugs from DrugBank database
 

  Details on drugs targeting PDE6B.
ID Name Drug Type Targets #Targets
DB00201CaffeineSmall MoleculeADORA1, ADORA2A, ATM, ITPR1, ITPR2, ITPR3, PDE10A, PDE11A, PDE1A, ......33
DB09283TrapidilSmall MoleculePDE10A, PDE11A, PDE1A, PDE1B, PDE1C, PDE2A, PDE3A, PDE3B, PDE4A, P ......21