Using the Pathway Tools Omics Viewer

Note: The Pathway Tools Omics Viewer was formerly known as the Pathway Tools Expression Viewer. It has recently been extended to display many other types of experimental data, not just gene expression data, so has been renamed.

The Pathway Tools Omics Viewer uses the Metabolic Overview for an organism to illustrate the results of high-throughput experiments in a global metabolic pathway context. Genes (in the case of a gene expression experiment) and proteins (in the case of a proteomics experiment) that are involved in metabolism are mapped to reaction steps in the Metabolic Overview, and the range of data values levels in a given experimental dataset is mapped to a spectrum of colors. Reaction steps in the Metabolic Overview are colored according to the corresponding data value. Similarly, for metabolomics experiments, compound nodes are colored according to the data value for the corresponding compound. This facility enables the user to see instantly which pathways are active or inactive under some set of experimental conditions.

The Omics Viewer can be used for: