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Establishing robust links among gene expression, pathways and phenotypes is critical for understanding diseases and developing treatments. In recent years there have been many efforts to develop the computational means to traverse from genes to gene expression, model pathways and classify phenotypes. Numerous ontologies and other controlled vocabularies have been developed, as well as computational methods to combine and mine these data sets and establish connections. Here we discuss these efforts and identify areas of future work that could lead to a better integration of genes, pathways and phenotypes to provide insights into the mechanisms under which gene mutations affect expression and pathways and how these effects are manifested onto the phenotype.   Electronic supplementary material  The online version of this article (doi:10.1186/s13326-015-0013-5) contains supplementary material, which is available to authorized users.

Linking gene expression to phenotypes via pathway information