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It is a curated collection of well-documented molecular reactions that span the gamut from simple intermediate metabolism (e.g., sugar catabolism) to complex cellular events such as the mitotic cell cycle. The Reactome project, covered in this unit, is one such database. Hence there is a high degree of interest in the bioinformatics community in creating pathway databases. For example, a microarray experiment that changes the expression pattern of thousands of genes may only affect the expression patterns of a small handful of biochemical pathways. They capture what is already known about the interplay of genes, proteins and small molecules using a data model that is accessible to computation. Biological pathway databases have come to play a key role in the interpretation of such data sets. This information explosion has been accelerated by the invention of high throughput techniques, such as next-generation DNA sequencing, RNA sequencing, expression microarrays (see Chapter 7), ChIP-chip, and ChIP-seq, which now allow biologists to generate huge experimental data sets that cannot easily be interpreted by simple inspection. The completion of multiple genomes in recent years has led to an explosion of information about known and predicted gene products.

This unit describes how to use the Reactome database to learn the steps of a biological pathway navigate and browse through the Reactome database identify the pathways in which a molecule of interest is involved use the Pathway and Expression analysis tools to search the database for and visualize possible connections within user-supplied experimental data set and Reactome pathways and the Species Comparison tool to compare human and model organism pathways.

This information is supplemented with likely orthologous molecular reactions in mouse, rat, zebrafish, worm and other model organisms. It is an expert-authored and peer-reviewed, curated collection of well-documented molecular reactions that span the gamut from simple intermediate metabolism to signaling pathways and complex cellular events.

The Reactome project (a collaboration between the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Medical Center and the European Bioinformatics Institute) is one such pathway database and collects structured information on all the biological pathways and processes in the human. There is considerable interest in the bioinformatics community in creating pathway databases.

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