Pathway Tools Omics ViewersNote: 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:
Click here to go to the Webinar page, where you can watch the Comparative and Omics Tools in BioCyc instructional videos.
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
Single Experiment Time Step or Animated Time SeriesTo 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.
Color SchemeData 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.
Choose a color scheme:
Display TypeBy 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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Page generated by Pathway Tools version 27.5 (software by SRI International) on Tue Feb 20, 2024, BIOCYC14A.
EcoCyc version 27.5.