Pathway Tools Omics Viewers

Note: This Omics Viewer will soon be retired. There is a new Omics Viewer as part of the Cellular Overview implementation, please see new Cellular Overview. The new Cellular Overview is accessible by the top menu bar command Tools→Cellular Overview. Please use that link instead.

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 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.

Click here to go to the Webinar page, where you can watch the Comparative and Omics Tools in BioCyc instructional videos.

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.

File containing experimental data (NOT a URL):
Do you want to display absolute or relative data values?
If displaying relative data values, use a single data column
the ratio of two data columns
Data values use a: 0-centered scale (e.g. log scale)
1-centered scale (negative values will be discarded)
The items in the first (zeroth) column of your datafile are
Note: By selecting Any of the above, you can combine, for example, gene expression and metabolomics data into a single display. There are some dangers inherent in this approach, however. Some names may be ambiguous if it is not known if they refer to genes, proteins or metabolites. In addition, data values from different kinds of experiments may not be directly comparable, so the resulting diagram may be misleading in some important ways.

Single Experiment Time Step or Animated Time Series

To display a single experiment time step, enter a single column number in one or both of the column number fields below.

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.

Data columns (numerators in ratios):
 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

Data values are divided into color bins, with the highest value bins displayed in red, the lowest value bins displayed in green or yellow, and the middle bins displayed in blue. Three color scheme options are available.
  • 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 threshold, yellow for data values less than the inverse of that threshold, and blue for values in between. The threshold 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 threshold:

Display Type

By default, data values are painted on the cellular overview chart. However an alternative display is to either paint data values on the genomic map, or to generate a table containing all individual pathways which have one or more data values that exceed some threshold (or are less than the inverse of that threshold). To select one of these alternative displays, choose the corresponding option below and specify the threshold if appropriate. Note that if both the cellular and genome overviews are specified, the genome overview will appear in a new browser window (you must have popups enabled for this site or this will not work).
Paint data on cellular overview chart (default)
Paint data on genome overview chart
Generate a table of individual pathways exceeding threshold:

Note: if you create a user account and log in, you can save your selections for next time.

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.

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