A biochemical cascade, also known as a signaling cascade or signaling pathway, is a series of chemical reactions that occur within a biological cell when initiated by a stimulus. This stimulus, known as a first messenger, acts on a receptor that is transduced to the cell interior through second messengers which amplify the signal and transfer it to effector molecules, causing the cell to respond to the initial stimulus.Most biochemical cascades are series of events, in which one event triggers the next, in a linear fashion. At each step of the signaling cascade, various controlling factors are involved to regulate cellular actions, in order to respond effectively to cues about their changing internal and external environments.
An example would be the coagulation cascade of secondary hemostasis which leads to fibrin formation, and thus, the initiation of blood coagulation. Another example, sonic hedgehog signaling pathway, is one of the key regulators of embryonic development and is present in all bilaterians.Signaling proteins give cells information to make the embryo develop properly. When the pathway malfunctions, it can result in diseases like basal cell carcinoma. Recent studies point to the role of hedgehog signaling in regulating adult stem cells involved in maintenance and regeneration of adult tissues. The pathway has also been implicated in the development of some cancers. Drugs that specifically target hedgehog signaling to fight diseases are being actively developed by a number of pharmaceutical companies.
Cells require a full and functional cellular machinery to live. When they belong to complex multicellular organisms, they need to communicate among themselves and work for symbiosis in order to give life to the organism. These communications between cells triggers intracellular signaling cascades, termed signal transduction pathways, that regulate specific cellular functions. Each signal transduction occurs with a primary extracellular messenger that binds to a transmembrane or nuclear receptor, initiating intracellular signals. The complex formed produces or releases second messengers that integrate and adapt the signal, amplifying it, by activating molecular targets, which in turn trigger effectors that will lead to the desired cellular response.
Signal transduction is realized by activation of specific receptors and consequent production/delivery of second messengers, such as Ca2+ or cAMP. These molecules operate as signal transducers, triggering intracellular cascades and in turn amplifying the initial signal.Two main signal transduction mechanisms have been identified, via nuclear receptors, or via transmembrane receptors. In the first one, first messenger cross through the cell membrane, binding and activating intracellular receptors localized at nucleus or cytosol, which then act as transcriptional factors regulating directly gene expression. This is possible due to the lipophilic nature of those ligands, mainly hormones. In the signal transduction via transmembrane receptors, the first messenger binds to the extracellular domain of transmembrane receptor, activating it. These receptors may have intrinsic catalytic activity or may be coupled to effector enzymes, or may also be associated to ionic channels. Therefore, there are four main transmembrane receptor types: G protein coupled receptors (GPCRs), tyrosine kinase receptors (RTKs), serine/threonine kinase receptors (RSTKs), and ligand-gated ion channels (LGICs). Second messengers can be classified into three classes:
The cellular response in signal transduction cascades involves alteration of the expression of effector genes or activation/inhibition of targeted proteins. Regulation of protein activity mainly involves phosphorylation/dephosphorylation events, leading to its activation or inhibition. It is the case for the vast majority of responses as a consequence of the binding of the primary messengers to membrane receptors. This response is quick, as it involves regulation of molecules that are already present in the cell. On the other hand, the induction or repression of the expression of genes requires the binding of transcriptional factors to the regulatory sequences of these genes. The transcriptional factors are activated by the primary messengers, in most cases, due to their function as nuclear receptors for these messengers. The secondary messengers like DAG or Ca2+ could also induce or repress gene expression, via transcriptional factors. This response is slower than the first because it involves more steps, like transcription of genes and then the effect of newly formed proteins in a specific target. The target could be a protein or another gene.
In biochemistry, several important enzymatic cascades and signal transduction cascades participate in metabolic pathways or signaling networks, in which enzymes are usually involved to catalyze the reactions. For example, the tissue factor pathway in the coagulation cascade of secondary hemostasis is the primary pathway leading to fibrin formation, and thus, the initiation of blood coagulation. The pathways are a series of reactions, in which a zymogen (inactive enzyme precursor) of a serine protease and its glycoprotein co-factors are activated to become active components that then catalyze the next reaction in the cascade, ultimately resulting in cross-linked fibrin.
Another example, sonic hedgehog signaling pathway, is one of the key regulators of embryonic development and is present in all bilaterians.Different parts of the embryo have different concentrations of hedgehog signaling proteins, which give cells information to make the embryo develop properly and correctly into a head or a tail. When the pathway malfunctions, it can result in diseases like basal cell carcinoma. Recent studies point to the role of hedgehog signaling in regulating adult stem cells involved in maintenance and regeneration of adult tissues. The pathway has also been implicated in the development of some cancers. Drugs that specifically target hedgehog signaling to fight diseases are being actively developed by a number of pharmaceutical companies. Most biochemical cascades are series of events, in which one event triggers the next, in a linear fashion.
Biochemical cascades include:
Conversely, negative cascades include events that are in a circular fashion, or can cause or be caused by multiple events.Negative cascades include:
Adhesion is an essential process to epithelial cells so that epithelium can be formed and cells can be in permanent contact with extracellular matrix and other cells. Several pathways exist to accomplish this communication and adhesion with environment. But the main signalling pathways are the cadherin and integrin pathways.The cadherin pathway is present in adhesion junctions or in desmosomes and it is responsible for epithelial adhesion and communication with adjacent cells. Cadherin is a transmembrane glycoprotein receptor that establishes contact with another cadherin present in the surface of a neighbour cell forming an adhesion complex. This adhesion complex is formed by β-catenin and α-catenin, and p120CAS is essential for its stabilization and regulation. This complex then binds to actin, leading to polymerization. For actin polymerization through the cadherin pathway, proteins of the Rho GTPases family are also involved. This complex is regulated by phosphorylation, which leads to downregulation of adhesion. Several factors can induce the phosphorylation, like EGF, HGF or v-Src. The cadherin pathway also has an important function in survival and proliferation because it regulates the concentration of cytoplasmic β-catenin. When β-catenin is free in the cytoplasm, normally it is degraded, however if the Wnt signalling is activated, β-catenin degradation is inhibited and it is translocated to the nucleus where it forms a complex with transcription factors. This leads to activation of genes responsible for cell proliferation and survival. So the cadherin-catenin complex is essential for cell fate regulation. Integrins are heterodimeric glycoprotein receptors that recognize proteins present in the extracellular matrix, like fibronectin and laminin. In order to function, integrins have to form complexes with ILK and Fak proteins. For adhesion to the extracellular matrix, ILK activate the Rac and Cdc42 proteins and leading to actin polymerization. ERK also leads to actin polymerization through activation of cPLA2. Recruitment of FAK by integrin leads to Akt activation and this inhibits pro-apoptotic factors like BAD and Bax. When adhesion through integrins do not occur the pro-apoptotic factors are not inhibited and resulting in apoptosis.
The hepatocyte is a complex and multifunctional differentiated cell whose cell response will be influenced by the zone in hepatic lobule, because concentrations of oxygen and toxic substances present in the hepatic sinusoids change from periportal zone to centrilobular zone10. The hepatocytes of the intermediate zone have the appropriate morphological and functional features since they have the environment with average concentrations of oxygen and other substances.This specialized cell is capable of:
The hepatocyte also regulates other functions for constitutive synthesis of proteins (albumin, ALT and AST) that influences the synthesis or activation of other molecules (synthesis of urea and essential amino acids), activate vitamin D, utilization of vitamin K, transporter expression of vitamin A and conversion of thyroxine.
Purinergic signalling has an essential role at interactions between neurons and glia cells, allowing these to detect action potentials and modulate neuronal activity, contributing for intra and extracellular homeostasis regulation. Besides purinergic neurotransmitter, ATP acts as a trophic factor at cellular development and growth, being involved on microglia activation and migration, and also on axonal myelination by oligodendrocytes. There are two main types of purinergic receptors, P1 binding to adenosine, and P2 binding to ATP or ADP, presenting different signalling cascades.The Nrf2/ARE signalling pathway has a fundamental role at fighting against oxidative stress, to which neurons are especially vulnerable due to its high oxygen consumption and high lipid content. This neuroprotective pathway involves control of neuronal activity by perisynaptic astrocytes and neuronal glutamate release, with the establishment of tripartite synapses. The Nrf2/ARE activation leads to a higher expression of enzymes involved in glutathione syntheses and metabolism, that have a key role in antioxidant response. The LKB1/NUAK1 signalling pathway regulates terminal axon branching at cortical neurons, via local immobilized mitochondria capture. Besides NUAK1, LKB1 kinase acts under other effectors enzymes as SAD-A/B and MARK, therefore regulating neuronal polarization and axonal growth, respectively. These kinase cascades implicates also Tau and others MAP. An extended knowledge of these and others neuronal pathways could provide new potential therapeutic targets for several neurodegenerative chronic diseases as Alzheimer's, Parkinson's and Huntington's disease, and also amyotrophic lateral sclerosis.
The blood cells (erythrocytes, leukocytes and platelets) are produced by hematopoiesis. The erythrocytes have as main function the O2 delivery to the tissues, and this transfer occurs by diffusion and is determined by the O2 tension (PO2). The erythrocyte is able to feel the tissue need for O2 and cause a change in vascular caliber, through the pathway of ATP release, which requires an increase in cAMP, and are regulated by the phosphodiesterase (PDE). This pathway can be triggered via two mechanisms: physiological stimulus (like reduced O2 tension) and activation of the prostacyclin receptor (IPR). This pathway includes heterotrimeric G proteins, adenylyl cyclase (AC), protein kinase A (PKA), cystic fibrosis transmembrane conductance regulator (CFTR), and a final conduit that transport ATP to vascular lumen (pannexin 1 or voltage-dependent anion channel (VDAC)). The released ATP acts on purinergic receptors on endothelial cells, triggering the synthesis and release of several vasodilators, like nitric oxide (NO) and prostacyclin (PGI2).The current model of leukocyte adhesion cascade includes many steps mentioned in Table 1. The integrin-mediated adhesion of leukocytes to endothelial cells is related with morphological changes in both leukocytes and endothelial cells, which together support leukocyte migration through the venular walls. Rho and Ras small GTPases are involved in the principal leukocyte signaling pathways underlying chemokine-stimulated integrin-dependent adhesion, and have important roles in regulating cell shape, adhesion and motility.
After a vascular injury occurs, platelets are activated by locally exposed collagen (glycoprotein (GP) VI receptor), locally generated thrombin (PAR1 and PAR4 receptors), platelet-derived thromboxane A2 (TxA2) (TP receptor) and ADP (P2Y1 and P2Y12 receptors) that is either released from damaged cells or secreted from platelet dense granules. The von Willebrand factor (VWF) serves as an essential accessory molecule. In general terms, platelet activation initiated by agonist takes to a signaling cascade that leads to an increase of the cytosolic calcium concentration. Consequently, the integrin αIIbβ3 is activated and the binding to fibrinogen allows the aggregation of platelets to each other. The increase of cytosolic calcium also leads to shape change and TxA2 synthesis, leading to signal amplification.
The main goal of biochemical cascades in lymphocytes is the secretion of molecules that can suppress altered cells or eliminate pathogenic agents, through proliferation, differentiation and activation of these cells. Therefore, the antigenic receptors play a central role in signal transduction in lymphocytes, because when antigens interact with them lead to a cascade of signal events. These receptors, that recognize the antigen soluble (B cells) or linked to a molecule on Antigen Presenting Cells (T cells), do not have long cytoplasm tails, so they are anchored to signal proteins, which contain a long cytoplasmic tails with a motif that can be phosphorylated (ITAM – immunoreceptor tyrosine-based activation motif) and resulting in different signal pathways. The antigen receptor and signal protein form a stable complex, named BCR or TCR, in B or T cells, respectively. The family Src is essential for signal transduction in these cells, because it is responsible for phosphorylation of ITAMs. Therefore, Lyn and Lck, in lymphocytes B and T, respectively, phosphorylate immunoreceptor tyrosine-based activation motifs after the antigen recognition and the conformational change of the receptor, which leads to the binding of Syk/Zap-70 kinases to ITAM and its activation. Syk kinase is specific of lymphocytes B and Zap-70 is present in T cells. After activation of these enzymes, some adaptor proteins are phosphorylated, like BLNK (B cells) and LAT (T cells). These proteins after phosphorylation become activated and allow binding of others enzymes that continue the biochemical cascade.One example of a protein that binds to adaptor proteins and become activated is PLC that is very important in the lymphocyte signal pathways. PLC is responsible for PKC activation, via DAG and Ca2+, which leads to phosphorylation of CARMA1 molecule, and formation of CBM complex. This complex activates Iκκ kinase, which phosphorylates I-κB, and then allows the translocation of NF-κB to the nucleus and transcription of genes encoding cytokines, for example. Others transcriptional factors like NFAT and AP1 complex are also important for transcription of cytokines. The differentiation of B cells to plasma cells is also an example of a signal mechanism in lymphocytes, induced by a cytokine receptor. In this case, some interleukins bind to a specific receptor, which leads to activation of MAPK/ERK pathway. Consequently, the BLIMP1 protein is translated and inhibits PAX5, allowing immunoglobulin genes transcription and activation of XBP1 (important for the secretory apparatus formation and enhancing of protein synthesis). Also, the coreceptors (CD28/CD19) play an important role because they can improve the antigen/receptor binding and initiate parallel cascade events, like activation o PI3 Kinase. PIP3 then is responsible for activation of several proteins, like vav (leads to activation of JNK pathway, which consequently leads to activation of c-Jun) and btk (can also activate PLC).
The Wnt signaling pathway can be divided in canonical and non-canonical. The canonical signaling involves binding of Wnt to Frizzled and LRP5 co-receptor, leading to GSK3 phosphorylation and inhibition of β-catenin degradation, resulting in its accumulation and translocation to the nucleus, where it acts as a transcription factor. The non-canonical Wnt signaling can be divided in planar cell polarity (PCP) pathway and Wnt/calcium pathway. It is characterized by binding of Wnt to Frizzled and activation of G proteins and to an increase of intracellular levels of calcium through mechanisms involving PKC 50.The Wnt signaling pathway plays a significative role in osteoblastogenesis and bone formation, inducing the differentiation of mesenquimal pluripotent cells in osteoblasts and inhibiting the RANKL/RANK pathway and osteoclastogenesis.
RANKL is a member of the TNF superfamily of ligands. Through binding to the RANK receptor it activates various molecules, like NF-kappa B, MAPK, NFAT and PI3K52. The RANKL/RANK signaling pathway regulates osteoclastogenesis, as well as, the survival and activation of osteoclasts.
Adenosine is very relevant in bone metabolism, as it plays a role in formation and activation of both osteoclasts and osteoblasts. Adenosine acts by binding to purinergic receptors and influencing adenylyl cyclase activity and the formation of cAMP and PKA 54.Adenosine may have opposite effects on bone metabolism, because while certain purinergic receptors stimulate adenylyl cyclase activity, others have the opposite effect. Under certain circumstances adenosine stimulates bone destruction and in other situations it promotes bone formation, depending on the purinergic receptor that is being activated.
Self-renewal and differentiation abilities are exceptional properties of stem cells. These cells can be classified by their differentiation capacity, which progressively decrease with development, in totipotents, pluripotents, multipotents and unipotents.
Self-renewal process is highly regulated from cell cycle and genetic transcription control. There are some signaling pathways, such as LIF/JAK/STAT3 (Leukemia inhibitory factor/Janus kinase/Signal transducer and activator of transcription 3) and BMP/SMADs/Id (Bone morphogenetic proteins/ Mothers against decapentaplegic/ Inhibitor of differentiation), mediated by transcription factors, epigenetic regulators and others components, and they are responsible for self-renewal genes expression and inhibition of differentiation genes expression, respectively.
At cell cycle level there is an increase of complexity of the mechanisms in somatic stem cells. However, it is observed a decrease of self-renewal potential with age. These mechanisms are regulated by p16Ink4a-CDK4/6-Rb and p19Arf-p53-P21 Cip1 signaling pathways. Embryonic stem cells have constitutive cyclin E-CDK2 activity, which hyperphosphorylates and inactivates Rb. This leads to a short G1 phase of the cell cycle with rapid G1-S transition and little dependence on mitogenic signals or D cyclins for S phase entry. In fetal stem cells, mitogens promote a relatively rapid G1-S transition through cooperative action of cyclin D-CDK4/6 and cyclin E-CDK2 to inactivate Rb family proteins. p16Ink4a and p19Arf expression are inhibited by Hmga2-dependent chromatin regulation. Many young adult stem cells are quiescent most of the time. In the absence of mitogenic signals, cyclin-CDKs and the G1-S transition are suppressed by cell cycle inhibitors including Ink4 and Cip/Kip family proteins. As a result, Rb is hypophosphorylated and inhibits E2F, promoting quiescence in G0-phase of the cell cycle. Mitogen stimulation mobilizes these cells into cycle by activating cyclin D expression. In old adult stem cells, let-7 microRNA expression increases, reducing Hmga2 levels and increasing p16Ink4a and p19Arf levels. This reduces the sensitivity of stem cells to mitogenic signals by inhibiting cyclin-CDK complexes. As a result, either stem cells cannot enter the cell cycle, or cell division slows in many tissues.
Extrinsic regulation is made by signals from the niche, where stem cells are found, which is able to promote quiescent state and cell cycle activation in somatic stem cells.Asymmetric division is characteristic of somatic stem cells, maintaining the reservoir of stem cells in the tissue and production of specialized cells of the same.
Stem cells show an elevated therapeutic potential, mainly in hemato-oncologic pathologies, such as leukemia and lymphomas. Little groups of stem cells were found into tumours, calling cancer stem cells. There are evidences that these cells promote tumor growth and metastasis.
The oocyte is the female cell involved in reproduction.There is a close relationship between the oocyte and the surrounding follicular cells which is crucial to the development of both. GDF9 and BMP15 produced by the oocyte bind to BMPR2 receptors on follicular cells activating SMADs 2/3, ensuring follicular development. Concomitantly, oocyte growth is initiated by binding of KITL to its receptor KIT in the oocyte, leading to the activation of PI3K/Akt pathway, allowing oocyte survival and development. During embryogenesis, oocytes initiate meiosis and stop in prophase I. This arrest is maintained by elevated levels of cAMP within the oocyte. It was recently suggested that cGMP cooperates with cAMP to maintain the cell cycle arrest. During meiotic maturation, the LH peak that precedes ovulation activates MAPK pathway leading to gap junction disruption and breakdown of communication between the oocyte and the follicular cells. PDE3A is activated and degrades cAMP, leading to cell cycle progression and oocyte maturation. The LH surge also leads to the production of progesterone and prostaglandins that induce the expression of ADAMTS1 and other proteases, as well as their inhibitors. This will lead to degradation of the follicular wall, but limiting the damage and ensuring that the rupture occurs in the appropriate location, releasing the oocyte into the Fallopian tubes. Oocyte activation depends on fertilization by sperm. It is initiated with sperm's attraction induced by prostaglandins produced by the oocyte, which will create a gradient that will influence the sperm's direction and velocity. After fusion with the oocyte, PLC ζ of the spermatozoa is released into the oocyte leading to an increase in Ca2+ levels that will activate CaMKII which will degrade MPF, leading to the resumption of meiosis. The increased Ca2+ levels will induce the exocytosis of cortical granules that degrade ZP receptors, used by sperm to penetrate the oocyte, blocking polyspermy. Deregulation of these pathways will lead to several diseases like, oocyte maturation failure syndrome which results in infertility. Increasing our molecular knowledge of oocyte development mechanisms could improve the outcome of assisted reproduction procedures, facilitating conception.
Spermatozoon is the male gamete. After ejaculation this cell is not mature, so it can not fertilize the oocyte. To have the ability to fertilize the female gamete, this cell suffers capacitation and acrosome reaction in female reproductive tract. The signaling pathways best described for spermatozoon involve these processes. The cAMP/PKA signaling pathway leads to sperm cells capacitation; however, adenylyl cyclase in sperm cells is different from the somatic cells. Adenylyl cyclase in spermatozoon does not recognize G proteins, so it is stimulated by bicarbonate and Ca2+ ions. Then, it converts adenosine triphosphate into cyclic AMP, which activates Protein kinase A. PKA leads to protein tyrosine phosphorylation.Phospholipase C (PLC) is involved in acrosome reaction. ZP3 is a glycoprotein present in zona pelucida and it interacts with receptors in spermatozoon. So, ZP3 can activate G protein coupled receptors and tyrosine kinase receptors, that leads to production of PLC. PLC cleaves the phospholipid phosphatidylinositol 4,5-bisphosphate (PIP2) into diacyl glycerol (DAG) and inositol 1,4,5-trisphosphate. IP3 is released as a soluble structure into the cytosol and DAG remains bound to the membrane. IP3 binds to IP3 receptors, present in acrosome membrane. In addition, calcium and DAG together work to activate protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. These actions cause an increase in cytosolic concentration of Ca2+ that leads to dispersion of actin and consequently promotes plasmatic membrane and outer acrosome membrane fusion. Progesterone is a steroid hormone produced in cumulus oophorus. In somatic cells it binds to receptors in nucleus; however, in spermatozoon its receptors are present in plasmatic membrane. This hormone activates AKT that leads to activation of other protein kinases, involved in capacitation and acrosome reaction. When ROS (reactive oxygen species) are present in high concentration, they can affect the physiology of cells, but when they are present in moderated concentration they are important for acrosome reaction and capacitation. ROS can interact with cAMP/PKA and progesterone pathway, stimulating them. ROS also interacts with ERK pathway that leads to activation of Ras, MEK and MEK-like proteins. These proteins activate protein tyrosine kinase (PTK) that phosphorylates various proteins important for capacitation and acrosome reaction.
Various signalling pathways, as FGF, WNT and TGF-β pathways, regulate the processes involved in embryogenesis.
FGF (Fibroblast Growth Factor) ligands bind to receptors tyrosine kinase, FGFR (Fibroblast Growth Factor Receptors), and form a stable complex with co-receptors HSPG (Heparan Sulphate Proteoglycans) that will promote autophosphorylation of the intracellular domain of FGFR and consequent activation of four main pathways: MAPK/ERK, PI3K, PLCγ and JAK/STAT.
The WNT pathway allows β-catenin function in gene transcription, once the interaction between WNT ligand and G protein-coupled receptor Frizzled inhibits GSK-3 (Glycogen Synthase Kinase-3) and thus formation of β-catenin destruction complex.Although there is some controversy about the effects of this pathway in embryogenesis, it is thought that WNT signalling induces primitive streak, mesoderm and endoderm formation. In TGF-β (Transforming Growth Factor β) pathway, BMP (Bone Morphogenic Protein), Activin and Nodal ligands bind to their receptors and activate Smads that bind to DNA and promote gene transcription. Activin is necessary for mesoderm and specially endoderm differentiation, and Nodal and BMP are involved in embryo patterning. BMP is also responsible for formation of extra-embryonic tissues before and during gastrulation, and for early mesoderm differentiation, when Activin and FGF pathways are activated.
Pathway building has been performed by individual groups studying a network of interest (e.g., immune signaling pathway) as well as by large bioinformatics consortia (e.g., the Reactome Project) and commercial entities (e.g., Ingenuity Systems). Pathway building is the process of identifying and integrating the entities, interactions, and associated annotations, and populating the knowledge base. Pathway construction can have either a data-driven objective (DDO) or a knowledge-driven objective (KDO). Data-driven pathway construction is used to generate relationship information of genes or proteins identified in a specific experiment such as a microarray study.Knowledge-driven pathway construction entails development of a detailed pathway knowledge base for particular domains of interest, such as a cell type, disease, or system. The curation process of a biological pathway entails identifying and structuring content, mining information manually and/or computationally, and assembling a knowledgebase using appropriate software tools. A schematic illustrating the major steps involved in the data-driven and knowledge-driven construction processes.
For either DDO or KDO pathway construction, the first step is to mine pertinent information from relevant information sources about the entities and interactions. The information retrieved is assembled using appropriate formats, information standards, and pathway building tools to obtain a pathway prototype. The pathway is further refined to include context-specific annotations such as species, cell/tissue type, or disease type. The pathway can then be verified by the domain experts and updated by the curators based on appropriate feedback.Recent attempts to improve knowledge integration have led to refined classifications of cellular entities, such as GO, and to the assembly of structured knowledge repositories. Data repositories, which contain information regarding sequence data, metabolism, signaling, reactions, and interactions are a major source of information for pathway building. A few useful databases are described in the following table.
|Database||Curation Type||GO Annotation (Y/N)||Description|
|1. Protein-protein interactions databases|
|BIND||Manual Curation||N||200,000 documented biomolecular interactions and complexes|
|MINT||Manual Curation||N||Experimentally verified interactions|
|HPRD||Manual Curation||N||Elegant and comprehensive presentation of the interactions, entities and evidences|
|MPact||Manual and Automated Curation||N||Yeast interactions. A part of MIPS|
|DIP [ permanent dead link ]||Manual and Automated Curation||Y||Experimentally determined interactions|
|IntAct||Manual Curation||Y||Database and analysis system of binary and multi-protein interactions|
|PDZBase||Manual Curation||N||PDZ Domain containing proteins|
|GNPV [ permanent dead link ]||Manual and Automated Curation||Y||Based on specific experiments and literature|
|BioGrid||Manual Curation||Y||Physical and genetic interactions|
|UniHi||Manual and Automated Curation||Y||Comprehensive human protein interactions|
|OPHID||Manual Curation||Y||Combines PPI from BIND, HPRD, and MINT|
|2. Metabolic Pathway databases|
|EcoCyc||Manual and Automated Curation||Y||Entire genome and biochemical machinery of E. Coli|
|MetaCyc||Manual Curation||N||Pathways of over 165 species|
|HumanCyc||Manual and Automated Curation||N||Human metabolic pathways and the human genome|
|BioCyc||Manual and Automated Curation||N||Collection of databases for several organism|
|3. Signaling Pathway databases|
|KEGG [ permanent dead link ]||Manual Curation||Y||Comprehensive collection of pathways such as human disease, signaling, genetic information processing pathways. Links to several useful databases|
|PANTHER||Manual Curation||N||Compendium of metabolic and signaling pathways built using CellDesigner. Pathways can be downloaded in SBML format|
|Reactome||Manual Curation||Y||Hierarchical layout. Extensive links to relevant databases such as NCBI, ENSEMBL, UNIPROT, HAPMAP, KEGG, CHEBI, PubMed, GO. Follows PSI-MI standards|
|Biomodels||Manual Curation||Y||Domain experts curated biological connection maps and associated mathematical models|
|STKE||Manual Curation||N||Repository of canonical pathways|
|Ingenuity Systems||Manual Curation||Y||Commercial mammalian biological knowledgebase about genes, drugs, chemical, cellular and disease processes, and signaling and metabolic pathways|
|Human signaling network||Manual Curation||Y||Literature-curated human signaling network, the largest human signaling network database|
|PID [ permanent dead link ]||Manual Curation||Y||Compendium of several highly structured, assembled signaling pathways|
|BioPP||Manual and Automated Curation||Y||Repository of biological pathways built using CellDesigner|
Legend: Y – Yes, N – No; BIND – Biomolecular Interaction Network Database, DIP – Database of Interacting Proteins, GNPV – Genome Network Platform Viewer, HPRD = Human Protein Reference Database, MINT – Molecular Interaction database, MIPS – Munich Information center for Protein Sequences, UNIHI – Unified Human Interactome, OPHID – Online Predicted Human Interaction Database, EcoCyc – Encyclopaedia of E. Coli Genes and Metabolism, MetaCyc – aMetabolic Pathway database, KEGG – Kyoto Encyclopedia of Genes and Genomes, PANTHER – Protein Analysis Through Evolutionary Relationship database, STKE – Signal Transduction Knowledge Environment, PID – The Pathway Interaction Database, BioPP – Biological Pathway Publisher. A comprehensive list of resources can be found at http://www.pathguide.org.
The increasing amount of genomic and molecular information is the basis for understanding higher-order biological systems, such as the cell and the organism, and their interactions with the environment, as well as for medical, industrial and other practical applications. The KEGG resourceprovides a reference knowledge base for linking genomes to biological systems, categorized as building blocks in the genomic space (KEGG GENES), the chemical space (KEGG LIGAND), wiring diagrams of interaction networks and reaction networks (KEGG PATHWAY), and ontologies for pathway reconstruction (BRITE database). The KEGG PATHWAY database is a collection of manually drawn pathway maps for metabolism, genetic information processing, environmental information processing such as signal transduction, ligand–receptor interaction and cell communication, various other cellular processes and human diseases, all based on extensive survey of published literature.
Gene Map Annotator and Pathway Profiler (GenMAPP)a free, open-source, stand-alone computer program is designed for organizing, analyzing, and sharing genome scale data in the context of biological pathways. GenMAPP database support multiple gene annotations and species as well as custom species database creation for a potentially unlimited number of species. Pathway resources are expanded by utilizing homology information to translate pathway content between species and extending existing pathways with data derived from conserved protein interactions and coexpression. A new mode of data visualization including time-course, single nucleotide polymorphism (SNP), and splicing, has been implemented with GenMAPP database to support analysis of complex data. GenMAPP also offers innovative ways to display and share data by incorporating HTML export of analyses for entire sets of pathways as organized web pages. In short, GenMAPP provides a means to rapidly interrogate complex experimental data for pathway-level changes in a diverse range of organisms.
Given the genetic makeup of an organism, the complete set of possible reactions constitutes its reactome. Reactome, located at http://www.reactome.org is a curated, peer-reviewed resource of human biological processes/pathway data. The basic unit of the Reactome database is a reaction; reactions are then grouped into causal chains to form pathwaysThe Reactome data model allows us to represent many diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, and signal transduction, and high-level processes, such as the cell cycle. Reactome provides a qualitative framework, on which quantitative data can be superimposed. Tools have been developed to facilitate custom data entry and annotation by expert biologists, and to allow visualization and exploration of the finished dataset as an interactive process map. Although the primary curational domain is pathways from Homo sapiens, electronic projections of human pathways onto other organisms are regularly created via putative orthologs, thus making Reactome relevant to model organism research communities. The database is publicly available under open source terms, which allows both its content and its software infrastructure to be freely used and redistributed. Studying whole transcriptional profiles and cataloging protein–protein interactions has yielded much valuable biological information, from the genome or proteome to the physiology of an organism, an organ, a tissue or even a single cell. The Reactome database containing a framework of possible reactions which, when combined with expression and enzyme kinetic data, provides the infrastructure for quantitative models, therefore, an integrated view of biological processes, which links such gene products and can be systematically mined by using bioinformatics applications. Reactome data available in a variety of standard formats, including BioPAX, SBML and PSI-MI, and also enable data exchange with other pathway databases, such as the Cycs, KEGG and amaze, and molecular interaction databases, such as BIND and HPRD. The next data release will cover apoptosis, including the death receptor signaling pathways, and the Bcl2 pathways, as well as pathways involved in hemostasis. Other topics currently under development include several signaling pathways, mitosis, visual phototransduction and hematopoeisis. In summary, Reactome provides high-quality curated summaries of fundamental biological processes in humans in a form of biologist-friendly visualization of pathways data, and is an open-source project.
In the post-genomic age, high-throughput sequencing and gene/protein profiling techniques have transformed biological research by enabling comprehensive monitoring of a biological system, yielding a list of differentially expressed genes or proteins, which is useful in identifying genes that may have roles in a given phenomenon or phenotype.With DNA microarrays and genome-wide gene engineering, it is possible to screen global gene expression profiles to contribute a wealth of genomic data to the public domain. With RNA interference, it is possible to distill the inferences contained in the experimental literature and primary databases into knowledge bases that consist of annotated representations of biological pathways. In this case, individual genes and proteins are known to be involved in biological processes, components, or structures, as well as how and where gene products interact with each other. Pathway-oriented approaches for analyzing microarray data, by grouping long lists of individual genes, proteins, and/or other biological molecules according to the pathways they are involved in into smaller sets of related genes or proteins, which reduces the complexity, have proven useful for connecting genomic data to specific biological processes and systems. Identifying active pathways that differ between two conditions can have more explanatory power than a simple list of different genes or proteins. In addition, a large number of pathway analytic methods exploit pathway knowledge in public repositories such as Gene Ontology (GO) or Kyoto Encyclopedia of Genes and Genomes (KEGG), rather than inferring pathways from molecular measurements. Furthermore, different research focuses have given the word "pathway" different meanings. For example, 'pathway' can denote a metabolic pathway involving a sequence of enzyme-catalyzed reactions of small molecules, or a signaling pathway involving a set of protein phosphorylation reactions and gene regulation events. Therefore, the term "pathway analysis" has a very broad application. For instance, it can refer to the analysis physical interaction networks (e.g., protein–protein interactions), kinetic simulation of pathways, and steady-state pathway analysis (e.g., flux-balance analysis), as well as its usage in the inference of pathways from expression and sequence data. Several functional enrichment analysis tools and algorithms have been developed to enhance data interpretation. The existing knowledge base–driven pathway analysis methods in each generation have been summarized in recent literature.
A program package MatchMiner was used to scan HUGO names for cloned genes of interest are scanned, then are input into GoMiner, which leveraged the GO to identify the biological processes, functions and components represented in the gene profile. Also, Database for Annotation, Visualization, and Integrated Discovery (DAVID) and KEGG database can be used for the analysis of microarray expression data and the analysis of each GO biological process (P), cellular component (C), and molecular function (F) ontology. In addition, DAVID tools can be used to analyze the roles of genes in metabolic pathways and show the biological relationships between genes or gene-products and may represent metabolic pathways. These two databases also provide bioinformatics tools online to combine specific biochemical information on a certain organism and facilitate the interpretation of biological meanings for experimental data. By using a combined approach of Microarray-Bioinformatic technologies, a potential metabolic mechanism contributing to colorectal cancer (CRC) has been demonstratedSeveral environmental factors may be involved in a series of points along the genetic pathway to CRC. These include genes associated with bile acid metabolism, glycolysis metabolism and fatty acid metabolism pathways, supporting a hypothesis that some metabolic alternations observed in colon carcinoma may occur in the development of CRC.
Cellular models are instrumental in dissecting a complex pathological process into simpler molecular events. Parkinson's disease (PD) is multifactorial and clinically heterogeneous; the aetiology of the sporadic (and most common) form is still unclear and only a few molecular mechanisms have been clarified so far in the neurodegenerative cascade. In such a multifaceted picture, it is particularly important to identify experimental models that simplify the study of the different networks of proteins and genes involved. Cellular models that reproduce some of the features of the neurons that degenerate in PD have contributed to many advances in our comprehension of the pathogenic flow of the disease. In particular, the pivotal biochemical pathways (i.e. apoptosis and oxidative stress, mitochondrial impairment and dysfunctional mitophagy, unfolded protein stress and improper removal of misfolded proteins) have been widely explored in cell lines, challenged with toxic insults or genetically modified. The central role of a-synuclein has generated many models aiming to elucidate its contribution to the dysregulation of various cellular processes. Classical cellular models appear to be the correct choice for preliminary studies on the molecular action of new drugs or potential toxins and for understanding the role of single genetic factors. Moreover, the availability of novel cellular systems, such as cybrids or induced pluripotent stem cells, offers the chance to exploit the advantages of an in vitro investigation, although mirroring more closely the cell population being affected.
Synaptic degeneration and death of nerve cells are defining features of Alzheimer's disease (AD), the most prevalent age-related neurodegenerative disorders. In AD, neurons in the hippocampus and basal forebrain (brain regions that subserve learning and memory functions) are selectively vulnerable. Studies of postmortem brain tissue from AD people have provided evidence for increased levels of oxidative stress, mitochondrial dysfunction and impaired glucose uptake in vulnerable neuronal populations. Studies of animal and cell culture models of AD suggest that increased levels of oxidative stress (membrane lipid peroxidation, in particular) may disrupt neuronal energy metabolism and ion homeostasis, by impairing the function of membrane ion-motive ATPases, glucose and glutamate transporters. Such oxidative and metabolic compromise may thereby render neurons vulnerable to excitotoxicity and apoptosis. Recent studies suggest that AD can manifest systemic alterations in energy metabolism (e.g., increased insulin resistance and dysregulation of glucose metabolism). Emerging evidence that dietary restriction can forestall the development of AD is consistent with a major "metabolic" component to these disorders, and provides optimism that these devastating brain disorders of aging may be largely preventable.
Signal transduction is the process by which a chemical or physical signal is transmitted through a cell as a series of molecular events, most commonly protein phosphorylation catalyzed by protein kinases, which ultimately results in a cellular response. Proteins responsible for detecting stimuli are generally termed receptors, although in some cases the term sensor is used. The changes elicited by ligand binding in a receptor give rise to a biochemical cascade, which is a chain of biochemical events known as a signaling pathway.
Paracrine signaling is a form of cell signaling, a type of cellular communication in which a cell produces a signal to induce changes in nearby cells, altering the behaviour of those cells. Signaling molecules known as paracrine factors diffuse over a relatively short distance, as opposed to cell signaling by endocrine factors, hormones which travel considerably longer distances via the circulatory system; juxtacrine interactions; and autocrine signaling. Cells that produce paracrine factors secrete them into the immediate extracellular environment. Factors then travel to nearby cells in which the gradient of factor received determines the outcome. However, the exact distance that paracrine factors can travel is not certain.
The MAPK/ERK pathway is a chain of proteins in the cell that communicates a signal from a receptor on the surface of the cell to the DNA in the nucleus of the cell.
Receptor tyrosine kinases (RTKs) are the high-affinity cell surface receptors for many polypeptide growth factors, cytokines, and hormones. Of the 90 unique tyrosine kinase genes identified in the human genome, 58 encode receptor tyrosine kinase proteins. Receptor tyrosine kinases have been shown not only to be key regulators of normal cellular processes but also to have a critical role in the development and progression of many types of cancer. Mutations in receptor tyrosine kinases lead to activation of a series of signalling cascades which have numerous effects on protein expression. Receptor tyrosine kinases are part of the larger family of protein tyrosine kinases, encompassing the receptor tyrosine kinase proteins which contain a transmembrane domain, as well as the non-receptor tyrosine kinases which do not possess transmembrane domains.
Platelet-derived growth factor receptors (PDGF-R) are cell surface tyrosine kinase receptors for members of the platelet-derived growth factor (PDGF) family. PDGF subunits -A and -B are important factors regulating cell proliferation, cellular differentiation, cell growth, development and many diseases including cancer. There are two forms of the PDGF-R, alpha and beta each encoded by a different gene. Depending on which growth factor is bound, PDGF-R homo- or heterodimerizes.
Microphthalmia-associated transcription factor also known as class E basic helix-loop-helix protein 32 or bHLHe32 is a protein that in humans is encoded by the MITF gene.
c-Jun is a protein that in humans is encoded by the JUN gene. c-Jun, in combination with c-Fos, forms the AP-1 early response transcription factor. It was first identified as the Fos-binding protein p39 and only later rediscovered as the product of the JUN gene. c-jun was the first oncogenic transcription factor discovered. The proto-oncogene c-Jun is the cellular homolog of the viral oncoprotein v-jun. The viral homolog v-jun was discovered in avian sarcoma virus 17 and was named for ju-nana, the Japanese word for 17. The human JUN encodes a protein that is highly similar to the viral protein, which interacts directly with specific target DNA sequences to regulate gene expression. This gene is intronless and is mapped to 1p32-p31, a chromosomal region involved in both translocations and deletions in human malignancies.
Activator protein 1 (AP-1) is a transcription factor that regulates gene expression in response to a variety of stimuli, including cytokines, growth factors, stress, and bacterial and viral infections. AP-1 controls a number of cellular processes including differentiation, proliferation, and apoptosis. The structure of AP-1 is a heterodimer composed of proteins belonging to the c-Fos, c-Jun, ATF and JDP families.
Apoptosis signal-regulating kinase 1 (ASK1) also known as mitogen-activated protein kinase 5 (MAP3K5) is a member of MAP kinase family and as such a part of mitogen-activated protein kinase pathway. It activates c-Jun N-terminal kinase (JNK) and p38 mitogen-activated protein kinases in a Raf-independent fashion in response to an array of stresses such as oxidative stress, endoplasmic reticulum stress and calcium influx. ASK1 has been found to be involved in cancer, diabetes, rheumatoid arthritis, cardiovascular and neurodegenerative diseases.
Mitogen-activated protein kinase 14, also called p38-α, is an enzyme that in humans is encoded by the MAPK14 gene.
Transforming protein RhoA, also known as Ras homolog family member A (RhoA), is a small GTPase protein in the Rho family of GTPases that in humans is encoded by the RHOA gene. While the effects of RhoA activity are not all well known, it is primarily associated with cytoskeleton regulation, mostly actin stress fibers formation and actomyosin contractility. It acts upon several effectors. Among them, ROCK1 and DIAPH1 are the best described. RhoA, and the other Rho GTPases, are part of a larger family of related proteins known as the Ras superfamily, a family of proteins involved in the regulation and timing of cell division. RhoA is one of the oldest Rho GTPases, with homologues present in the genomes since 1.5 billion years. As a consequence, RhoA is somehow involved in many cellular processes which emerged throughout evolution. RhoA specifically is regarded as a prominent regulatory factor in other functions such as the regulation of cytoskeletal dynamics, transcription, cell cycle progression and cell transformation.
Serine/threonine-protein kinase PAK 1 is an enzyme that in humans is encoded by the PAK1 gene.
DNA damage-inducible transcript 3, also known as C/EBP homologous protein (CHOP), is a pro-apoptotic transcription factor that is encoded by the DDIT3 gene. It is a member of the CCAAT/enhancer-binding protein (C/EBP) family of DNA-binding transcription factors. The protein functions as a dominant-negative inhibitor by forming heterodimers with other C/EBP members, preventing their DNA binding activity. The protein is implicated in adipogenesis and erythropoiesis, and has an important role in the cell's stress response.
Mitogen-activated protein kinase kinase kinase kinase 4 (MAP4K4) – also known as hepatocyte progenitor kinase-like/germinal center kinase-like kinase (HGK) and Nck-interacting kinase (NIK) – is an enzyme, specifically a serine/threonine (S/T) kinase encoded by the MAP4K4 gene in humans.
Mitogen-activated protein kinase 15, also known as MAPK15, ERK7, or ERK8, is an enzyme that in humans is encoded by the MAPK15 gene.
The Akt signaling pathway or PI3K-Akt signaling pathway is a signal transduction pathway that promotes survival and growth in response to extracellular signals. Key proteins involved are PI3K and Akt.
Forkhead box protein O1 (FOXO1), also known as forkhead in rhabdomyosarcoma (FKHR), is a protein that in humans is encoded by the FOXO1 gene. FOXO1 is a transcription factor that plays important roles in regulation of gluconeogenesis and glycogenolysis by insulin signaling, and is also central to the decision for a preadipocyte to commit to adipogenesis. It is primarily regulated through phosphorylation on multiple residues; its transcriptional activity is dependent on its phosphorylation state.
The Hippo signaling pathway, also known as the Salvador-Warts-Hippo (SWH) pathway, is a signaling pathway that controls organ size in animals through the regulation of cell proliferation and apoptosis. The pathway takes its name from one of its key signaling components—the protein kinase Hippo (Hpo). Mutations in this gene lead to tissue overgrowth, or a "hippopotamus"-like phenotype.
Activity-regulated cytoskeleton-associated protein is a plasticity protein that in humans is encoded by the ARC gene. It was first characterized in 1995. ARC is a member of the immediate-early gene (IEG) family, a rapidly activated class of genes functionally defined by their ability to be transcribed in the presence of protein synthesis inhibitors. ARC mRNA is localized to activated synaptic sites in an NMDA receptor-dependent manner, where the newly translated protein is believed to play a critical role in learning and memory-related molecular processes. Arc protein is widely considered to be important in neurobiology because of its activity regulation, localization, and utility as a marker for plastic changes in the brain. Dysfunction in the production of Arc protein has been implicated as an important factor in understanding various neurological conditions, including amnesia, Alzheimer's disease, Autism spectrum disorders, and Fragile X syndrome. Along with other IEGs such as ZNF268 and HOMER1, ARC is also a significant tool for systems neuroscience as illustrated by the development of the cellular compartment analysis of temporal activity by fluorescence in situ hybridization, or catFISH technique.
The interleukin-1 receptor (IL-1R) associated kinase (IRAK) family plays a crucial role in the protective response to pathogens introduced into the human body by inducing acute inflammation followed by additional adaptive immune responses. IRAKs are essential components of the Interleukin-1 receptor signaling pathway and some Toll-like receptor signaling pathways. Toll-like receptors (TLRs) detect microorganisms by recognizing specific pathogen-associated molecular patterns (PAMPs) and IL-1R family members respond the interleukin-1 (IL-1) family cytokines. These receptors initiate an intracellular signaling cascade through adaptor proteins, primarily, MyD88. This is followed by the activation of IRAKs. TLRs and IL-1R members have a highly conserved amino acid sequence in their cytoplasmic domain called the Toll/Interleukin-1 (TIR) domain. The elicitation of different TLRs/IL-1Rs results in similar signaling cascades due to their homologous TIR motif leading to the activation of mitogen-activated protein kinases (MAPKs) and the IκB kinase (IKK) complex, which initiates a nuclear factor-κB (NF-κB) and AP-1-dependent transcriptional response of pro-inflammatory genes. Understanding the key players and their roles in the TLR/IL-1R pathway is important because the presence of mutations causing the abnormal regulation of Toll/IL-1R signaling leading to a variety of acute inflammatory and autoimmune diseases.