However, all of these efforts are let down by one or a number of key factors. Using these tools it is possible to view a range of canonical pathway views or generate networks of interactions based on a given query. Recent years have seen considerable growth in the availability of public and commercial databases offering searchable access to pathways and interaction data derived from a combination of manual and automated (text mining) extraction of primary literature, reviews and large-scale molecular interaction studies. Whilst they are clearly useful aids to understanding cellular events, even at their best, they are not sufficient by themselves, relying on extensive textual descriptions to explain what is shown pictorially. Traditionally, representations of molecular pathways have been produced ad hoc and frequently included in reviews and original papers. However without such models we can not hope to truly understand biology at a systems level. ![]() Whilst our ability to perform quantitative and qualitative measurements on the cellular components has increased massively in recent years, as has our knowledge on how they interact with each other, we still struggle to translate these observations into graphical and computationally tractable models. In this context, pathways may be defined as a network of directional interactions between the components of a cell which orchestrate an appropriate shift in cellular activity in response to a specific biological input or event. The innate immune response is executed at the molecular level by a complex series of interwoven signalling pathways. Furthermore, we discuss issues with the limitations and scalability of pathways presented in this fashion, explore options for automated layout of large pathway networks and demonstrate how such maps can aid the interpretation of functional studies. The map presents a powerful visual aid for interpreting the available pathway interaction knowledge and underscores the valuable contribution well constructed pathway diagrams make to communicating large amounts of molecular interaction data. The pathway map is available in a number of electronic formats and editing is supported by yEd graph editor software. ![]() Here we describe the construction of a logically represented pathway diagram which attempts to integrate these four pathways central to innate immunity using a modified version of the Edinburgh Pathway Notation. However, these pathways are commonly viewed as separate entities rather than an integrated network of molecular interactions. Four key signalling cascades triggered early-on in the innate immune response are the toll-like receptor, interferon, NF-κB and apoptotic pathways, which co-operate to defend cells against a given pathogen. The molecular regulation of this response has been studied in great detail but comprehensive and unambiguous diagrams describing these events are generally unavailable. The complex yet flexible cellular response to pathogens is orchestrated by the interaction of multiple signalling and metabolic pathways.
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