Gene Report

Basic Information

Approved Symbol	PDE1B
Approved Name	phosphodiesterase 1B, calmodulin-dependent
Previous Symbol	PDES1B
Location	12q13
Position	chr12:54971644-54973023 (+)
External Links	Entrez Gene: 5153 Ensembl: ENSG00000123360 UCSC: uc001sgd.2 HGNC ID: 8775
No. of Studies (Positive/Negative)	1(1/0)
Type	Literature-origin

Positive relationships between PDE1B and MDD (count: 0)

Positive relationships between PDE1B and other components at different levels (count: 1)

Genetic/epigenetic locus					Protein and other molecule			Cell and molecular pathway			Neural system			Cognition and behavior		Symptoms and signs			Environment

Name in Literature	Level	Approved Name (Name in Literature)	Type	Reference	Research Type	Statistical Result	Relation Description	All
Name in Literature	Related Components
Pde1b		SLC17A7(vesicular glutamate transporter 1 (VGLUT1))	gene	Tordera RM, 2011	animal model		gene was regulated in frontal cortex of VGLUT1(+/-) mice gene was regulated in frontal cortex of VGLUT1(+/-) mice

Positive relationship network of PDE1B in MK4MDD

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Note:
1. The different color of the nodes denotes the level of the nodes.

Genetic/Epigenetic Locus	Protein and Other Molecule	Cell and Molecular Pathway	Neural System	Cognition and Behavior	Symptoms and Signs	Environment	MDD

2. Besides the component related relationships from literature, gene mapped protein and protein mapped gene are also shown in the network. If the mapped gene or protein is not from literature, square node would be used instead of Circle node. Accordingly, the relationship is marked with dot line.
2. User can drag the nodes to rearrange the layout of the network. Click the node will enter the report page of the node. Right-click will show also the menus to link to the report page of the node and remove the node and related edges. Hover the node will show the level of the node and hover the edge will show the evidence/description of the edge.
3. The network is generated using Cytoscape Web

Negative relationships between PDE1B and MDD (count: 0)

Negative relationships between PDE1B and other components at different levels (count: 0)

PDE1B related SNPs in MK4MDD (count: 0)

PDE1B related proteins in MK4MDD (count: 0)

PDE1B related GO terms (count: 27)

ID	Name	Type	Evidence
Literature-origin GO terms
GO:0006915	apoptotic process	biological process	TAS[8855339]

ID	Name	Type	Evidence
Gene mapped GO terms
GO:0008542	visual learning	biological process	IEA
GO:0046069	cGMP catabolic process	biological process	IDA[14687666]
GO:0097011	cellular response to granulocyte macrophage colony-stimulating factor stimulus	biological process	IDA[14687666]
GO:0005829	cytosol	cellular component	TAS
GO:0048101	calcium- and calmodulin-regulated 3',5'-cyclic-GMP phosphodiesterase activity	molecular function	IEA
GO:0042053	regulation of dopamine metabolic process	biological process	IEA
GO:0007596	blood coagulation	biological process	TAS
GO:0006198	cAMP catabolic process	biological process	IDA[14687666]
GO:0004115	3',5'-cyclic-AMP phosphodiesterase activity	molecular function	IEA
GO:0030224	monocyte differentiation	biological process	IEP[14687666]
GO:0045087	innate immune response	biological process	TAS
GO:0005516	calmodulin binding	molecular function	IEA
GO:0007626	locomotory behavior	biological process	IEA
GO:0048011	neurotrophin TRK receptor signaling pathway	biological process	TAS
GO:0043025	neuronal cell body	cellular component	IEA
GO:0007202	activation of phospholipase C activity	biological process	TAS
GO:0036006	cellular response to macrophage colony-stimulating factor stimulus	biological process	IDA[14687666]
GO:0007173	epidermal growth factor receptor signaling pathway	biological process	TAS
GO:0007165	signal transduction	biological process	TAS
GO:0001505	regulation of neurotransmitter levels	biological process	IEA
GO:0005515	protein binding	molecular function	IPI[21044950]
GO:0004117	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity	molecular function	TAS[9419816]
GO:0001975	response to amphetamine	biological process	IEA
GO:0046872	metal ion binding	molecular function	IEA
GO:0042428	serotonin metabolic process	biological process	IEA
GO:0008543	fibroblast growth factor receptor signaling pathway	biological process	TAS

PDE1B related KEGG pathways (count: 2)

ID	Name	Brief Description	Full Description
Literature-origin KEGG pathway
hsa04020	calcium signaling_pathway	Calcium signaling pathway	Ca2+ that enters the cell from the outside is a principal so...... Ca2+ that enters the cell from the outside is a principal source of signal Ca2+. Entry of Ca2+ is driven by the presence of a large electrochemical gradient across the plasma membrane. Cells use this external source of signal Ca2+ by activating various entry channels with widely different properties. The voltage-operated channels (VOCs) are found in excitable cells and generate the rapid Ca2+ fluxes that control fast cellular processes. There are many other Ca2+-entry channels, such as the receptor-operated channels (ROCs), for example the NMDA (N-methyl-D-aspartate) receptors (NMDARs) that respond to glutamate. There also are second-messenger-operated channels (SMOCs) and store-operated channels (SOCs). The other principal source of Ca2+ for signalling is the internal stores that are located primarily in the endoplasmic/sarcoplasmic reticulum (ER/SR), in which inositol-1,4,5-trisphosphate receptors (IP3Rs) or ryanodine receptors (RYRs) regulate the release of Ca2+. The principal activator of these channels is Ca2+ itself and this process of Ca2+-induced Ca2+ release is central to the mechanism of Ca2+ signalling. Various second messengers or modulators also control the release of Ca2+. IP3, which is generated by pathways using different isoforms of phospholipase C (PLCbeta, delta, epsilon, gamma and zeta), regulates the IP3Rs. Cyclic ADP-ribose (cADPR) releases Ca2+ via RYRs. Nicotinic acid adenine dinucleotide phosphate (NAADP) may activate a distinct Ca2+ release mechanism on separate acidic Ca2+ stores. Ca2+ release via the NAADP-sensitive mechanism may also feedback onto either RYRs or IP3Rs. cADPR and NAADP are generated by CD38. This enzyme might be sensitive to the cellular metabolism, as ATP and NADH inhibit it. The influx of Ca2+ from the environment or release from internal stores causes a very rapid and dramatic increase in cytoplasmic calcium concentration, which has been widely exploited for signal transduction. Some proteins, such as troponin C (TnC) involved in muscle contraction, directly bind to and sense Ca2+. However, in other cases Ca2+ is sensed through intermediate calcium sensors such as calmodulin (CALM). More...

ID	Name	Brief Description	Full Description
Gene mapped KEGG pathways
hsa00230	purine metabolism	Purine metabolism

PDE1B related BioCarta pathways (count: 0)

PDE1B related Reactome pathways (count: 8)

ID	Name	Description
Gene mapped Reactome pathways
REACT_11061	signalling by_ngf	Neurotrophins (NGF, BDNF, NT-3, NT-4/5) play pivotal roles i...... Neurotrophins (NGF, BDNF, NT-3, NT-4/5) play pivotal roles in survival, differentiation, and plasticity of neurons in the peripheral and central nervous system. They are produced, and secreted in minute amounts, by a variety of tissues. They signal through two types of receptors: TRK tyrosine kinase receptors (TRKA, TRKB, TRKC), which specifically interact with the different neurotrophins, and p75NTR, which interacts with all neurotrophins. TRK receptors are reported in a variety of tissues in addition to neurons. p75NTRs are also widespread. Neurotrophins and their receptors are synthesized as several different splice variants, which differ in terms of their biological activities. The nerve growth factor (NGF) was the first growth factor to be identified and has served as a model for studying the mechanisms of action of neurotrophins and growth factors. The mechanisms by which NGF generates diverse cellular responses have been studied extensively in the rat pheochromocytoma cell line PC12. When exposed to NGF, PC12 cells exit the cell cycle and differentiate into sympathetic neuron-like cells. Current data show that signalling by the other neurotrophins is similar to NGF signalling. More...
REACT_15295	opioid signalling	Opioids are chemical substances similar to opiates, the acti...... Opioids are chemical substances similar to opiates, the active substances found in opium (morphine, codeine etc.). Opioid action is mediated by the receptors for endogenous opioids; peptides such as the enkephalins, the endorphins or the dynorphins. Opioids possess powerful analgesic and sedative effects, and are widely used as pain-killers. Their main side-effect is the rapid establishment of a strong addiction. Opioids receptors are G-protein coupled receptors (GPCR). There are four classes of receptors: mu (MOR), kappa (KOR) and delta (DOR), and the nociceptin receptor (NOP). More...
REACT_12056	trka signalling_from_the_plasma_membrane	Trk receptors signal from the plasma membrane and from intra...... Trk receptors signal from the plasma membrane and from intracellular membranes, particularly from early endosomes. Signalling from the plasma membrane is fast but transient; signalling from endosomes is slower but long lasting. Signalling from the plasma membrane is annotated here. TRK signalling leads to proliferation in some cell types and neuronal differentiation in others. Proliferation is the likely outcome of short term signalling, as observed following stimulation of EGFR (EGF receptor). Long term signalling via TRK receptors, instead, was clearly shown to be required for neuronal differentiation in response to neurotrophins. More...
REACT_15426	plc beta_mediated_events	The phospholipase C (PLC) family of enzymes is both diverse ...... The phospholipase C (PLC) family of enzymes is both diverse and complex. The isoforms beta, gamma and delta (each have subtypes) make up the members of this family. PLC hydrolyzes phosphatidylinositol bisphosphate (PIP2) into two second messengers, inositol 1,4,5-trisphosphate (IP3) and diacylglycerol (DAG). IP3 mobilizes intracellular calcium stores while DAG activates protein kinase C isoforms which are involved in regulatory functions. More...
REACT_12079	plc gamma1_signalling	The activation of phosphlipase C-gamma (PLC-gamma) and subse...... The activation of phosphlipase C-gamma (PLC-gamma) and subsequent mobilization of calcium from intracellular stores are essential for neurotrophin secretion. PLC-gamma is activated through the phosphorylation by TrkA receptor kinase and this form hydrolyses PIP2 to generate inositol tris-phosphate (IP3) and diacylglycerol (DAG). IP3 promotes the release of Ca2+ from internal stores and this results in activation of enzymes such as protein kinase C and Ca2+ calmodulin-regulated protein kinases. More...
REACT_19184	downstream events_in_gpcr_signaling	G protein-coupled receptors. The beta:gamma G-protein dimer ...... G protein-coupled receptors. The beta:gamma G-protein dimer is also involved in downstream signaling , and some receptors form part of metastable complexes of receptor and accessory proteins such as the arrestins. GPCRs are involved in many diverse signaling events , using a variety of pathways that include modulation of adenylyl cyclase, phospholipase C, the mitogen activated protein kinases (MAPKs), extracellular signal regulated kinase (ERK) c-Jun-NH2-terminal kinase (JNK) and p38 MAPK. More...
REACT_9053	cam pathway	Calmodulin (CaM) is a small acidic protein that contains fou...... Calmodulin (CaM) is a small acidic protein that contains four EF-hand motifs, each of which can bind a calcium ion, therefore it can bind up to four calcium ions. The protein has two approximately symmetrical domains, separated by a flexible hinge region. Calmodulin is the prototypical example of the EF-hand family of Ca2+-sensing proteins. Changes in intracellular Ca2+ concentration regulate calmodulin in three distinct ways. First, by directing its subcellular distribution. Second, by promoting association with different target proteins. Third, by directing a variety of conformational states in calmodulin that result in target-specific activation. Calmodulin binds and activates several effector protein (e.g. the CaM-dependent adenylyl cyclases, phosphodiesterases, protein kinases and the protein phosphatase calcineurin). More...
REACT_19327	g alpha_s_signalling_events	The general function of the G alpha (s) subunit (Gs) is to a...... The general function of the G alpha (s) subunit (Gs) is to activate adenylate cyclase, which in turn produces cAMP, leading to the activation of cAMP-dependent protein kinases (often referred to collectively as Protein Kinase A). The signal from the ligand-stimulated GPCR is amplified because the receptor can activate several Gs heterotrimers before it is inactivated. More...

PDE1B related interactors from protein-protein interaction data in HPRD (count: 0)

Gene Report

Literature-origin GO terms

Gene mapped GO terms

Literature-origin KEGG pathway

Gene mapped KEGG pathways

Gene mapped Reactome pathways