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. embryos 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. mapk/erk (mitogen-activated protein kinase/extracellular signal-regulated kinase) regulates gene transcription through successive kinase phosphorylation and in human embryonic stem cells it helps maintaining pluripotency. however, in the presence of activin a, a tgf-β ligand, it causes the formation of mesoderm and neuroectoderm. phosphorylation of membrane phospholipids by pi3k (phosphatidylinositol 3-kinase) results in activation of akt/pkb (protein kinase b). this kinase is involved in cell survival and inhibition of apoptosis, cellular growth and maintenance of pluripotency, in embryonic stem cells. plcγ (phosphoinositide phospholipase c γ) hydrolyzes membrane phospholipids to form ip3 (inositoltriphosphate) and dag (diacylglycerol), leading to activation of kinases and regulating morphogenic movements during gastrulation and neurulation. stat (signal trandsducer and activator of transcription) is phosphorylated by jak (janus kinase) and regulates gene transcription, determining cell fates. in mouse embryonic stem cells, this pathway helps maintaining pluripotency. 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 construction 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. databasecuration typego annotation (y/n)description 1. protein-protein interactions databases bindmanual curationn200,000 documented biomolecular interactions and complexes mintmanual curationnexperimentally verified interactions hprdmanual curationnelegant and comprehensive presentation of the interactions, entities and evidences mpactmanual and automated curationnyeast interactions. a part of mips dipmanual and automated curationyexperimentally determined interactions intactmanual curationydatabase and analysis system of binary and multi-protein interactions pdzbasemanual curationnpdz domain containing proteins gnpvmanual and automated curationybased on specific experiments and literature biogridmanual curationyphysical and genetic interactions unihimanual and automated curationycomprehensive human protein interactions ophidmanual curationycombines ppi from bind, hprd, and mint 2. metabolic pathway databases ecocycmanual and automated curationyentire genome and biochemical machinery of e. coli metacycmanual curationnpathways of over 165 species humancycmanual and automated curationnhuman metabolic pathways and the human genome biocycmanual and automated curationncollection of databases for several organism 3. signaling pathway databases keggmanual curationycomprehensive collection of pathways such as human disease, signaling, genetic information processing pathways. links to several useful databases panthermanual curationncompendium of metabolic and signaling pathways built using celldesigner. pathways can be downloaded in sbml format reactomemanual curationyhierarchical layout. extensive links to relevant databases such as ncbi, ensembl, uniprot, hapmap, kegg, chebi, pubmed, go. follows psi-mi standards biomodelsmanual curationydomain experts curated biological connection maps and associated mathematical models stkemanual curationnrepository of canonical pathways ingenuity systemsmanual curationycommercial mammalian biological knowledgebase about genes, drugs, chemical, cellular and disease processes, and signaling and metabolic pathways human signaling networkmanual curationyliterature-curated human signaling network, the largest human signaling network database pidmanual curationycompendium of several highly structured, assembled signaling pathways bioppmanual and automated curationyrepository 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. pathway-related databases and tools kegg 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 resource provides 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. genmapp 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. reactome 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 pathways the 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. pathway-oriented approaches 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