Pathway Tools Omics Viewer

Category Cross-Omics>Pathway Analysis/Tools

Abstract The Pathway Tools Omics Viewer (formerly the Pathway Tools Expression Viewer) paints data values from the user's high- throughput and other experiments onto the ‘Cellular Overview’ diagram for an organism.

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:

1) Microarray Expression Data -- Reaction lines (and protein icons, where present) are color-coded according to the relative or absolute expression level of the gene that codes for the enzyme that catalyzes that reaction step.

The Omics Viewer allows a scientist to interpret the results of ‘gene expression’ experiments in a pathway context.

2) Proteomics Data -- Reaction lines (and protein icons, where present) are color-coded according to the concentration of the enzyme that catalyzes that reaction step.

3) Metabolomics Data -- Compound icons are color-coded according to the concentration of the compound.

4) Reaction Flux Data -- Reaction lines are color-coded according to reaction flux values.

5) Other Experimental Data -- Any experiment, high-throughput or otherwise, in which data values are assigned to genes, proteins, reactions or metabolites can be viewed in a pathway context using the Omics Viewer.

The Omics Viewer can show absolute data values (such as the concentration of a metabolite or protein, or the absolute expression level of a gene), or it can be used to compare two (2) sets of experimental data by computing a ratio and mapping the ratios onto a color spectrum.

The superposition of multiple sets of experimental data on the ‘metabolic overview’ can also be animated to show, for example, how 'gene expression' levels of enzymes change with time over the course of an experiment.

Omics Viewer Results --

After you submit your dataset to the Pathway Tools system, the Omics Viewer returns the following results:

1) The Overview Diagram, colorized with experimental data.

2) The color key for the Overview.

3) For single experiments, some basic statistics are computed from the data file. The system counts and lists gene/protein/metabolite names that could Not be resolved, or for which data was missing or malformed. Since, for example, Not all genes will code for enzymes, and therefore Not all will correspond to reactions in the ‘Metabolic Overview’, SRI compiles separate statistics for only those that are represented in the Overview and for the dataset as a whole.

The statistics that SRI computes and tabulates are: number of values, minimum, maximum and median values, and mean and standard deviation of the natural logs of the values.

Note: These statistics are Not computed when generating animations.

4) A histogram that shows the distribution of values in the dataset. This histogram is displayed directly beneath the color key. The data value range is divided into 50 intervals, using the same criteria that SRI uses for assigning colors.

The number of data values in each interval is shown on the histogram, colored appropriately.

To the left of the vertical axis is the histogram for the entities that are represented in the overview. To the right of the axis is the histogram for all other entities in the dataset.

Animation Controls --

A ‘time series’ can be displayed as an animation by specifying multiple data column numbers. The result will be a Dynamic HTML page that initially plays the animation in a continuous loop, showing how the experimental values and histogram change with each experiment. Four (4) buttons control the animation. They can be used to stop and restart the animation and step through the individual time points.

System Requirements

See G6G Abstract Number 20230 or BioCyc


Manufacturer Web Site Pathway Tools Omics Viewer

Price Free for academic institutions. Fee required for commercial use. Licence required.

G6G Abstract Number 20237

G6G Manufacturer Number 102506