- Course overview
- Search within this course
- Why do we need a pathway database?
- When to use Reactome
- Who is Reactome for?
- Navigating Reactome
- Understanding the Pathway Browser
- Analysing data
- Programmatic access
- Contributing to Reactome
- Summary
- Try it yourself!
- Your feedback
- Get help and support on Reactome
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Foundation of Reactome
What is a biological pathway?
Cells contain many thousands of molecules, mostly proteins and small chemical compounds. Groups of molecules work together to perform tasks, e.g. provide energy, produce materials, respond to the environment, etc.
A biological pathway is an ordered series of molecular events that leads to the creation of a new molecular product, or a change in a cellular state or process (an example is shown in Figure 2). For example, a pathway could manufacture a protein, signal the presence of a hormonal signal, or cause a cell to move.
Why are pathways significant?
- A healthy cell (body) has many processes (pathways) that must all work together
- Faulty pathways can result in diseases such as cancer, asthma or diabetes. Most diseases are the result of small faults in several pathways, adding up to a problem that the body is unable to correct
- Medicines can correct faulty pathways, often by switching a signaling pathway on/off
- About 30% of all medicines act on a family of signaling proteins called G protein-coupled receptors (GPCRs). These medicines are worth an estimated 118 billion US dollars a year
Reactions (or pathway steps) are the units of Reactome
The units of Reactome are reactions. They can be thought of as steps in a pathway. Reactome uses the word reaction in a broad sense; any event that changes the state of a molecule is considered to be a reaction, not only classical biochemical reactions. Some examples are given in Figure 3.
Reactions connect to form pathways
Reactions can connect with other reactions, for example when the output of one becomes the input to another (Figure 4). Reactions that are connected may be grouped together, forming a named (canonical) pathway. Pathways may branch into sub-pathways or be cyclical. They are a convenient way to group events but it is important to understand that they do not occur in isolation. In pathway diagrams, a reaction output may not be an input to another reaction but it might be involved in another pathway. Reactions may also be present in more than one pathway. Some pathways are contained (encapsulated) in several larger pathways.
