Pathways are cellular procedures that carry out specific functions in the cell, such as amino acid synthesis and degradation, energy metabolism, signal transduction and more. This chapter discusses methods for pathway analysis and prediction. Metabolic pathways are pathways which consist mostly of enzymatic reactions. The supervised approach to automated metabolic pathway reconstruction is to create a metabolic network graph from known enzymatic reactions and chemical rules. Expression data is an important source of information on the activity of genes, which can help to assess the relevance of different genes in each pathway. The chapter focuses on the role of expression data in prediction based on pathway blueprints. A pathway can be viewed as a generic graph diagram or a blueprint, where the nodes of the graph are the locations in the pathway, annotated with just the function associated with each location.