Pathway Tools Omics Viewer

The Omics Viewer can be used for:

• 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.
• Proteomics Data: Reaction lines (and protein icons, where present) are color-coded according to the concentration of the enzyme that catalyzes that reaction step.
• Metabolomics Data: Compound icons are color-coded according to the concentration of the compound.
• Reaction Flux Data: Reaction lines are color-coded according to reaction flux values.
• 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.

More information about the Omics Viewer, including sample datafiles and displays.

The Omics Viewer takes as input a tab-delimited data file that is stored on your local computer. The file contains relative or absolute data for a set of genes, proteins, reactions, metabolites, or some combination. Each row of the file contains data for a single gene, protein, reaction, or metabolite, and begins with the object name, ID or EC number. You may choose to display either data from a single column, the ratio of two columns, or a time series animation of multiple columns. Data columns other than those specified are ignored.

For an example data file, see here

In addition to the color-coded Cellular Overview diagram, the resulting display includes a histogram and basic statistics computed from the supplied data.

Single Experiment Time Step or Animated Time Series

To display an animated time series, enter a list of column numbers (with each column number corresponding to a single timepoint), one per line, in the first column number field below. If you wish to include a denominator column for a ratio calculation, you can enter either a single column number (in which case the same data column will be used as the denominator for all timepoints), or one column number for each numerator column number. Note that zoomed views of individual pathways are not available with animations.

Data column (numerator in ratios):	If using two columns, denominator data column:
Note: For column numbering purposes, the first column, which contains the gene name, is column number 0. The first potential data column is column number 1.

Color Scheme

• By default, the color bins range over the entire spectrum, and the cutoff values for the color bins are derived from the data itself. This means that different experiments could be displayed using different color schemes, making it difficult to directly compare them.
• Alternatively, you may specify a value for the maximum value cutoff bin. All displays that use the same maximum value cutoff will use the same color scheme (assuming other settings, such as relative vs absolute, or log format vs non-log format are the same), and are therefore directly comparable. The maximum cutoff value should be a number, e.g. 2 or 10, etc. All data values greater than the maximum cutoff value will be displayed in red.
• The third alternative is to use only three color bins: red for data values that exceed some threshhold, yellow for data values less than the inverse of that threshhold, and blue for values in between. The threshhold value should be a number, e.g. 2 or 10.

Choose a color scheme:
Full color spectrum, computed from data provided (default)
Full color spectrum with a maximum cutoff:
Three color display with specified threshhold:

Display Type

Note that this request will take several minutes to complete (possibly longer for large datasets). For faster operation, install Pathway Tools on your own computer! Click here for details.