a(CHEBI:"calcium(2+)")
Because FKBP1b is a negative regulator of hippocampal neuronal Ca2 transients PubMed:29255009
It was demonstrated that Aβ42 oligomers, but not monomers, significantly altered Ca2+ release from intracellular stores (Lazzari et al. 2015), what induced intracellular Ca2+ increase in neurons via the complex PrPC–mGluR5, with harmful effects on synaptic transmission (Beraldo et al. 2016). PubMed:29196815
Excessive activation of NMDAR by soluble AβOs triggers disproportionate influx of Ca2+ into neurons, which leads to excitotoxicity, mitochondrial dysfunction, and loss of synapses (Zhao et al. 2004). PubMed:29196815
Long before the identification of the high Ca2+ permeability of alpha7 nAChR channels, different studies reported significant Ca2+ influx through nAChRs in muscle, parasympathetic neurons, pheochromocytoma cells, and human neuroblastoma cells (115, 321, 347, 407, 411, 459, 468). PubMed:19126755
For example, during a low degree of activation of alpha7 and alpha3beta4 nAChRs, Ca2+ can enter the cells through nAChRs or NMDA receptors and favor activation (i.e., phosphorylation) of the transcription factor CREB, which in turn modifies gene expression (82). PubMed:19126755
Long before the identification of the high Ca2+ permeability of alpha7 nAChR channels, different studies reported significant Ca2+ influx through nAChRs in muscle, parasympathetic neurons, pheochromocytoma cells, and human neuroblastoma cells (115, 321, 347, 407, 411, 459, 468). PubMed:19126755
For example, during a low degree of activation of alpha7 and alpha3beta4 nAChRs, Ca2+ can enter the cells through nAChRs or NMDA receptors and favor activation (i.e., phosphorylation) of the transcription factor CREB, which in turn modifies gene expression (82). PubMed:19126755
It has been shown that the alpha7 receptors, but not the alpha3beta2 receptors, specifically trigger calcium release from intracellular stores by activating ryanodine receptors. Such a specific functional coupling of alpha7 receptors and ryanodine-sensitive stores may provide another site of therapeutic intervention. However, the sustained calcium rise seen in these cells upon prolonged nicotine administration, which is more likely to be of relevance to neuroprotection than short-term responses, is more dependent upon the activation of inositol 1,4,5-triphosphate receptors (Dajas-Bailador et al., 2002a), which are also a target for phosphorylation by FYN (Cui et al., 2004). PubMed:19293145
Abeta1–42 activates heterologously expressed nAChRs (Dineley et al., 2002), and Abeta25–35 has been shown to activate non-alpha7 nAChRs in rat basal forebrain neurons (Fu and Jhamandas, 2003) and to evoke a alpha7- mediated calcium increases in presynaptic terminals isolated from rat hippocampus and neocortex (Dougherty et al., 2003). PubMed:19293145
Stevens et al. (2003) showed that calcineurin is involved in nicotine neuroprotection. Abeta, through alpha7 nAChRs, increases Ca2+, which phosphorylates NMDARs via calcineurin and protein tyrosine phosphatase, nonreceptor type 5 (striatum-enriched) (Snyder et al., 2005). PubMed:19293145
It has been shown that the alpha7 receptors, but not the alpha3beta2 receptors, specifically trigger calcium release from intracellular stores by activating ryanodine receptors. Such a specific functional coupling of alpha7 receptors and ryanodine-sensitive stores may provide another site of therapeutic intervention. However, the sustained calcium rise seen in these cells upon prolonged nicotine administration, which is more likely to be of relevance to neuroprotection than short-term responses, is more dependent upon the activation of inositol 1,4,5-triphosphate receptors (Dajas-Bailador et al., 2002a), which are also a target for phosphorylation by FYN (Cui et al., 2004). PubMed:19293145
This calcium influx can trigger calcium-induced calcium release from intracellular stores (86). PubMed:17009926
Nicotinic receptors mediate a small direct calcium influx (42–44, 85). PubMed:17009926
Similarly, replacement of the α7 leucine at the synaptic, extracellular end (position 254 or 255) of the pore by threonine dramatically reduced the calcium permeability of the α7 receptors. PubMed:17009926
Similarly, replacement of the α7 leucine at the synaptic, extracellular end (position 254 or 255) of the pore by threonine dramatically reduced the calcium permeability of the α7 receptors. PubMed:17009926
Similarly, replacement of the α7 leucine at the synaptic, extracellular end (position 254 or 255) of the pore by threonine dramatically reduced the calcium permeability of the α7 receptors. PubMed:17009926
Similarly, replacement of the α7 leucine at the synaptic, extracellular end (position 254 or 255) of the pore by threonine dramatically reduced the calcium permeability of the α7 receptors. PubMed:17009926
All the mammalian neuronal nAChR subtypes do share the general func- tional property of being permeable to small monovalent and divalent cations. The main conducting species under biological conditions are Na+, K+, and Ca2+. PubMed:26472524
All the mammalian neuronal nAChR subtypes do share the general func- tional property of being permeable to small monovalent and divalent cations. The main conducting species under biological conditions are Na+, K+, and Ca2+. PubMed:26472524
Stimulation of nicotinic receptors present at the CNS presynaptic neuronal membrane leads to an increase in presynaptic Ca2+ concentration, which may facilitate the release of a number of neurotransmitters, such as glutamate, GABA, dopamine, serotonin, norepinephrine, as well as ACh PubMed:26813123
PC12 cells transfected with α7345–348A showed a reduction in choline-mediated calcium responses. PubMed:26088141
As shown in Fig. 5, A–C, nifedipine was found to decrease the peak calcium response to choline in PC12 cells (peak: 795.00% ΔF/Fθ ± 107.1%) by 56.94% (p = 0.003), whereas prolonging the duration of the choline-induced calcium transient (AUC: 749.50% ΔF/Fθ2 × s ± 64.02%) in the same cell. PubMed:26088141
In α7345–348A nAChR expressing cells, nifedipine had no effect on the peak or the duration of the calcium transient (peak: 957.00% ΔF/Fθ ± 252.2%; AUC: 333.33% ΔF/Fθ2 × s ± 91.53%) relative to choline treatment alone (Fig. 5, A–C). The findings suggest that choline-induced calcium responses in PC12 cells involve the activity of VGCC (37, 38). PubMed:26088141
SP pretreatment did not significantly alter calcium peaks in α7345–348A nAChR expressing cells, showing a small (−31.24%) reduction in calcium responses relative to the α7345–348A baseline measure (p > 0.05). PubMed:26088141
PC12 cells transfected with α7345–348A showed a reduction in choline-mediated calcium responses. PubMed:26088141
Xestospongin C treatment did not impact the calcium peak (628.87% ΔF/Fθ ± 69.43%) or total calcium transient (AUC: 443.86% ΔF/Fθ2 × s ± 54.72%; + xestospongin C = 340.39% ΔF/Fθ2 × s ± 96.99%) in α7345–348A expressing cells (α7 to α7 + xestospongin C, p = 0.017; α7 to α7345–348A, p = 0.013; α7 to α7345-348A + xestospongin C, p = 0.017) (Fig. 7, B and C). The data underscores the inability of α7345–348A nAChRs to activate intracellular calcium via IP3Rs (18). PubMed:26088141
In α7+ cells, choline application resulted in a calcium signal that peaked at 1050% ΔF/Fθ (±176.4%) in the neurite. Calcium transients in the GC were found to last for ∼1.6 s in both α7 and α7+ cells peaking at 1396% (±154.4%) and 1316% (±146.9%) ΔF/Fθ, relatively (Fig. 4, A and B). PubMed:26088141
In N2a cells α7345–348A nAChR expression fostered a weak calcium response to (10 mM) choline, whereas expression of α7 nAChRs correlated with noticeable choline-induced calcium transient. Imaging studies in N2a cells expressing α7345–348A nAChRs indicate a significantly lowered calcium signal peak to choline (333.4% ΔF/Fθ ± 35.7%) when compared with N2a cells that express the α7nAChR (peak: 581% ΔF/Fθ ± 122.7%; p = 0.04) (Fig. 4, D and E). PubMed:26088141
Most notably, in the GC, the calcium peak values were significantly lower in α7345–348A-transfected cells compared with α7 cells after Tukey's HSD post hoc comparisons (peak: 741 ± 159.8% ΔF/Fθ, p = 0.006). This represents a 46.92% reduction from the α7 baseline calcium response (Fig. 4, A and B). This reduction approached significance in the neurite of α7345–348A cells (peak: 561 ± 124.9% ΔF/Fθ) (Fig. 4, A and B) PubMed:26088141
In N2a cells α7345–348A nAChR expression fostered a weak calcium response to (10 mM) choline, whereas expression of α7 nAChRs correlated with noticeable choline-induced calcium transient. Imaging studies in N2a cells expressing α7345–348A nAChRs indicate a significantly lowered calcium signal peak to choline (333.4% ΔF/Fθ ± 35.7%) when compared with N2a cells that express the α7nAChR (peak: 581% ΔF/Fθ ± 122.7%; p = 0.04) (Fig. 4, D and E). PubMed:26088141
The incubation with S 24795 was able to normalize Ca++ influx mediated by both alpha7 nAChR and NMDAR (Wang et al., 2009, 2010) PubMed:25514383
The incubation with S 24795 was able to normalize Ca++ influx mediated by both alpha7 nAChR and NMDAR (Wang et al., 2009, 2010) PubMed:25514383
In a different study, rat hippocampus and cortex were investigated and the activation of both alpha7 and non-alpha7 receptors was obtained with an enhancement of Ca++ influx into the neuron following the application of picomolar (pM) concentrations of Abeta1-42 PubMed:25514383
The incubation with S 24795 was able to normalize Ca++ influx mediated by both alpha7 nAChR and NMDAR (Wang et al., 2009, 2010) PubMed:25514383
This kinase is sensitive to Ca++, whose levels are increased following nAChR activation (Oddo et al., 2005) PubMed:25514383
As a consequence of nAChR hypersensitivity, lynx1 knockout mice display increased levels of Ca2+ in neurons, enhancements in synaptic efficacy, and improved learning and memory functions (Miwa et al., 2006; Darvas et al., 2009; Tekinay et al., 2009) PubMed:21482353
Since α7 AChRs are highly permeable to calcium [198] and increased calcium permeability is required for neuronal migration [199], neurons with less α7 AChRs would fail to migrate to their correct destinations [200] and be activated by acetylcholine. PubMed:22040696
Subsequently, renewed searches for functions of natural Bgt-binding nAChRs uncovered short-lived, nicotine-gated, toxin-sensitive, inward currents and/ or elevations of intracellular Ca2+ in chick autonomic neurons [84], in human ganglionic neuron-like clonal cells [85], or in rat CNS neurons [16,40–44,86–91]. PubMed:21787755
Dysfunctional membranes can also have an important impact on calcium homeostasis; some types of oligomers can lead to a cytotoxic calcium influx presumably by building pore-like structures [30]. PubMed:28803412
1 nM (Fig. 3a, right panels and Fig. 3b, red curve, solid line) and 0.2 nM α -syn fibrils (Fig. 3b, red curve, dashed line) induced a progressive and significant increase of intracellular Ca2+ levels, as revealed by the rise of Fluo-4 fluorescence in exposed SH-SY5Y cells. In contrast, only a modest Ca2+ increase was observed in cells exposed to 300 nM on-fibrillar assembly pathway oligomeric α -syn (Fig. 3a, middle panels and Fig. 3b, blue curve, solid line) or 10 μM monomeric α -syn (Fig. 3a, left panels and Fig. 3b, black curve, solid line). PubMed:27075649
1 nM (Fig. 3a, right panels and Fig. 3b, red curve, solid line) and 0.2 nM α -syn fibrils (Fig. 3b, red curve, dashed line) induced a progressive and significant increase of intracellular Ca2+ levels, as revealed by the rise of Fluo-4 fluorescence in exposed SH-SY5Y cells. In contrast, only a modest Ca2+ increase was observed in cells exposed to 300 nM on-fibrillar assembly pathway oligomeric α -syn (Fig. 3a, middle panels and Fig. 3b, blue curve, solid line) or 10 μM monomeric α -syn (Fig. 3a, left panels and Fig. 3b, black curve, solid line). PubMed:27075649
Fourth, activation of the lysosomal Ca 2+ channel mucol- ipin transient receptor potential channel 1 (TRPML1) with a synthetic agonist (ML-SA1) increased lysoso- mal Ca 2+ release, lowered pH and promoted Aβ clear- ance 191,192 . PubMed:30116051
Excitotoxicity leading to elevated intracellular calcium is a common feature of neurodegenerative diseases, and is implicated in AD (49, 50). This process may lead to enhanced activation of calpains (51). This in turn could influence a number of pathologic processes, including tau proteolysis. Indeed, tau has a number of putative calpain cleavage sites, and incubation of recombinant tau with calpain generates specific fragments, including one that is ∼35 kDa and one that is ∼17 kDa (19, 20). PubMed:24027553
Tau may be endocytosed, promoting an increase in intracellular calcium that results in neuronal death PubMed:28420982
For these studies, SH-SY5Y cells stably overexpressing tTG were used. tTG coimmunoprecipitated with tau, and elevating intracellular calcium levels with maitotoxin resulted in a 52 +/- 4% increase in the amount of tTG that coimmunoprecipitated with tau. The increase in association of tTG with tau after treatment with maitotoxin corresponded to a coimmunolocalization of tTG, tTG activity, and tau in the cells. Further, tau was modified by tTG in situ in response to maitotoxin treatment. In vitro polyaminated tau was significantly less susceptible to micro-calpain proteolysis; however, tTG-mediated polyamination of tau did not significantly alter the microtubule-binding capacity of tau. PubMed:10537045
Only middle-aged Tet-mev-1 mice showed JNK/MARK activation and Ca2+ overload, particularly in astrocytes with decreased hippocampal GFAP and S100ß, but without pathological features such as apoptosis, amyloidosis, and lactic acidosis in neurons and astrocytes. This led to decreasing levels of glial fibrillary acidic protein and S100β in the hippocampal area. PubMed:27623715
For these studies, SH-SY5Y cells stably overexpressing tTG were used. tTG coimmunoprecipitated with tau, and elevating intracellular calcium levels with maitotoxin resulted in a 52 +/- 4% increase in the amount of tTG that coimmunoprecipitated with tau. The increase in association of tTG with tau after treatment with maitotoxin corresponded to a coimmunolocalization of tTG, tTG activity, and tau in the cells. Further, tau was modified by tTG in situ in response to maitotoxin treatment. In vitro polyaminated tau was significantly less susceptible to micro-calpain proteolysis; however, tTG-mediated polyamination of tau did not significantly alter the microtubule-binding capacity of tau. PubMed:10537045
Another regulator of Ca2+, namely C/EPB-homologous protein (CHOP; also known as DDIT3), has been implicated in NLRP3 inflammasome activation89 PubMed:23702978
The mobilized Ca2+ has many molecular targets, including TGFβ-activated kinase 1 (TAK1; also known as MAP3K7) (REF. 86). PubMed:23702978
This channel senses intracellular ROS and responds by opening itself to facilitate Ca2+ influx into the cell; this is intriguing considering that both ion fluxes and the oxidative state (see below) have important roles in NLRP3 inflammasome activation. PubMed:23702978
Emerging evidence has implicated Amyloid-β in augmenting cytosolic Ca2+ levels and causing NF- κB activation via calcineurin in astrocytes PubMed:28745240
For example, during a low degree of activation of alpha7 and alpha3beta4 nAChRs, Ca2+ can enter the cells through nAChRs or NMDA receptors and favor activation (i.e., phosphorylation) of the transcription factor CREB, which in turn modifies gene expression (82). PubMed:19126755
There is evidence that anandamide is produced by postsynaptic neurons in response to elevated intracellular Ca2+ levels. For instance, concomitant activation of alpha7 nAChRs and NMDA receptors triggers the production of anandamine in postsynaptic neurons (448). Anandamine, then, functions as a retrograde messenger and regulates synaptic transmission by interacting with specific receptors in the presynaptic neurons/terminals (498). PubMed:19126755
It was then recognized that Ca2+ flux directly through nAChR channels or indirectly via voltage-gated Ca2+ channels is relevant for nicotinic modulation of transmitter release, synaptic plasticity, as well as neuronal viability, differentiation, and migration. PubMed:19126755
It was then recognized that Ca2+ flux directly through nAChR channels or indirectly via voltage-gated Ca2+ channels is relevant for nicotinic modulation of transmitter release, synaptic plasticity, as well as neuronal viability, differentiation, and migration. PubMed:19126755
It was then recognized that Ca2+ flux directly through nAChR channels or indirectly via voltage-gated Ca2+ channels is relevant for nicotinic modulation of transmitter release, synaptic plasticity, as well as neuronal viability, differentiation, and migration. PubMed:19126755
It was then recognized that Ca2+ flux directly through nAChR channels or indirectly via voltage-gated Ca2+ channels is relevant for nicotinic modulation of transmitter release, synaptic plasticity, as well as neuronal viability, differentiation, and migration. PubMed:19126755
It has been shown that the alpha7 receptors, but not the alpha3beta2 receptors, specifically trigger calcium release from intracellular stores by activating ryanodine receptors. Such a specific functional coupling of alpha7 receptors and ryanodine-sensitive stores may provide another site of therapeutic intervention. However, the sustained calcium rise seen in these cells upon prolonged nicotine administration, which is more likely to be of relevance to neuroprotection than short-term responses, is more dependent upon the activation of inositol 1,4,5-triphosphate receptors (Dajas-Bailador et al., 2002a), which are also a target for phosphorylation by FYN (Cui et al., 2004). PubMed:19293145
One group of modulators includes Ca2+, which potentiates most neuronal nAChRs (99, 100) and binds to the extracellular domain below the ACh site at residues contributed from both sides of the subunit interface (96). Another includes Zn2 . PubMed:23038257
This calcium influx can trigger calcium-induced calcium release from intracellular stores (86). PubMed:17009926
While nAChR activity causes depolarization, the divalent cation permeability plays an impor- tant physiological role by supplying ionic signals, including calcium (Bertrand, Galzi, Devillers-Thiery, Bertrand, & Changeux, 1993b; Dani & Bertrand, 2007; Decker & Dani, 1990; Gray, Rajan, Radcliffe, Yakehiro, & Dani, 1996; McGehee, Heath, Gelber, Devay, & Role, 1995; Vernino et al., 1992). PubMed:26472524
Although calcium modulation can act intracellularly, nAChRs also are allosterically modulated by extracellular calcium, leading to dramatic changes in the channel opening probability (Amador & Dani, 1995; Mulle, Lena, & Changeux, 1992; Vernino et al., 1992). PubMed:26472524
Stimulation of nicotinic receptors present at the CNS presynaptic neuronal membrane leads to an increase in presynaptic Ca2+ concentration, which may facilitate the release of a number of neurotransmitters, such as glutamate, GABA, dopamine, serotonin, norepinephrine, as well as ACh PubMed:26813123
Stimulation of nicotinic receptors present at the CNS presynaptic neuronal membrane leads to an increase in presynaptic Ca2+ concentration, which may facilitate the release of a number of neurotransmitters, such as glutamate, GABA, dopamine, serotonin, norepinephrine, as well as ACh PubMed:26813123
Stimulation of nicotinic receptors present at the CNS presynaptic neuronal membrane leads to an increase in presynaptic Ca2+ concentration, which may facilitate the release of a number of neurotransmitters, such as glutamate, GABA, dopamine, serotonin, norepinephrine, as well as ACh PubMed:26813123
Stimulation of nicotinic receptors present at the CNS presynaptic neuronal membrane leads to an increase in presynaptic Ca2+ concentration, which may facilitate the release of a number of neurotransmitters, such as glutamate, GABA, dopamine, serotonin, norepinephrine, as well as ACh PubMed:26813123
Stimulation of nicotinic receptors present at the CNS presynaptic neuronal membrane leads to an increase in presynaptic Ca2+ concentration, which may facilitate the release of a number of neurotransmitters, such as glutamate, GABA, dopamine, serotonin, norepinephrine, as well as ACh PubMed:26813123
Stimulation of nicotinic receptors present at the CNS presynaptic neuronal membrane leads to an increase in presynaptic Ca2+ concentration, which may facilitate the release of a number of neurotransmitters, such as glutamate, GABA, dopamine, serotonin, norepinephrine, as well as ACh PubMed:26813123
Moreover,nicotinic receptors can also be regulated allosterically by Ca2+ PubMed:26813123
In α7345–348A nAChR expressing cells, nifedipine had no effect on the peak or the duration of the calcium transient (peak: 957.00% ΔF/Fθ ± 252.2%; AUC: 333.33% ΔF/Fθ2 × s ± 91.53%) relative to choline treatment alone (Fig. 5, A–C). The findings suggest that choline-induced calcium responses in PC12 cells involve the activity of VGCC (37, 38). PubMed:26088141
Most neuronal nAChRs, including alpha4beta2 and alpha7, are potentiated by Ca2+ at millimolar concentrations50. PubMed:19721446
Most neuronal nAChRs, including alpha4beta2 and alpha7, are potentiated by Ca2+ at millimolar concentrations50. PubMed:19721446
Since α7 AChRs are highly permeable to calcium [198] and increased calcium permeability is required for neuronal migration [199], neurons with less α7 AChRs would fail to migrate to their correct destinations [200] and be activated by acetylcholine. PubMed:22040696
Calpains are calcium-activated cytosolic cysteine proteases. Two isoforms differentiated and named by their sensitivities to calcium (i.e., μ-calpain and m-calpain, also called calpain-1 and calpain-2) are abundant in the central nervous system, and respond to micromolar and millimolar concentrations of calcium, respectively (45). Calpain has been implicated in a number of neurodegenerative diseases [for a review, see (46)]. PubMed:24027553
Excitotoxicity leading to elevated intracellular calcium is a common feature of neurodegenerative diseases, and is implicated in AD (49, 50). This process may lead to enhanced activation of calpains (51). This in turn could influence a number of pathologic processes, including tau proteolysis. Indeed, tau has a number of putative calpain cleavage sites, and incubation of recombinant tau with calpain generates specific fragments, including one that is ∼35 kDa and one that is ∼17 kDa (19, 20). PubMed:24027553
Increasing intracellular calcium levels in PC12 cells leads to calpain-induced cleavage of tau (18). This may reflect a potential effect of excitotoxicity in AD. Inducing apoptosis in cerebellar granule cells yields calpain-mediated tau fragments, including a dominant ∼17 kDa fragment (17). PubMed:24027553
These findings provide new insights into the regulation of microtubule assembly, since Ca2+/calmodulin inhibition of tubulin polymerization into microtubules could be mediated by the direct binding of calmodulin to tau, thus preventing the interaction of this latter protein with tubulin. PubMed:2123288
We here confirmed the interaction of SlOOb with tau through affinity chromatography and crosslinking and demonstrated that such an interaction also inhibited mode I phosphorylation by a Ca2+/CaM-dependent kinase. Increasing Ca2+c oncentration to the 100 μM range potentiated the SlOOb effect. Therefore, although Ca2+-independent interactions may occur between SlOOb and protein tau, it is the Ca2+ form of SlOOb that has significant affinity for protein tau. In any case, Znz+ and Ca2+ both appear to be capabble of inducing a conformation in SlOOb that promotes its binding to target proteinins, including tau. PubMed:2833519
For these studies, SH-SY5Y cells stably overexpressing tTG were used. tTG coimmunoprecipitated with tau, and elevating intracellular calcium levels with maitotoxin resulted in a 52 +/- 4% increase in the amount of tTG that coimmunoprecipitated with tau. The increase in association of tTG with tau after treatment with maitotoxin corresponded to a coimmunolocalization of tTG, tTG activity, and tau in the cells. Further, tau was modified by tTG in situ in response to maitotoxin treatment. In vitro polyaminated tau was significantly less susceptible to micro-calpain proteolysis; however, tTG-mediated polyamination of tau did not significantly alter the microtubule-binding capacity of tau. PubMed:10537045
The mobilized Ca2+ has many molecular targets, including TGFβ-activated kinase 1 (TAK1; also known as MAP3K7) (REF. 86). PubMed:23702978
This channel senses intracellular ROS and responds by opening itself to facilitate Ca2+ influx into the cell; this is intriguing considering that both ion fluxes and the oxidative state (see below) have important roles in NLRP3 inflammasome activation. PubMed:23702978
BEL Commons is developed and maintained in an academic capacity by Charles Tapley Hoyt and Daniel Domingo-Fernández at the Fraunhofer SCAI Department of Bioinformatics with support from the IMI project, AETIONOMY. It is built on top of PyBEL, an open source project. Please feel free to contact us here to give us feedback or report any issues. Also, see our Publishing Notes and Data Protection information.
If you find BEL Commons useful in your work, please consider citing: Hoyt, C. T., Domingo-Fernández, D., & Hofmann-Apitius, M. (2018). BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. Database, 2018(3), 1–11.