The PMN enables users to display and analyze their experimental results on a Metabolic Map using the Omics Viewer tool.

• AraCyc Omics Viewer
• PoplarCyc Omics Viewer
• * Please note that this feature is not available for multispecies databases, including PlantCyc

Instructions for preparing an input file and using the Metabolic (Cellular) Overview and Omics Viewer are available.

You can test these resources out using species-specific sample data files that include different types of input data

AraCyc Sample Data Files

AraCyc Omics sample file 1

This file contains 6 columns of transcript expression data taken at different time points. There are positive and negative values and they represent relative expression levels.

• To view the first time point:
• Items in the first column of the file are: Gene names and/or identifiers
• Data column(s) to use: 1
• Data values use a: 0-centered scale
• Select type of values: Relative
• Choose a color scheme: Full color spectrum from data
• For relative data values use: No ratio of data columns


• To view the all time points in an animation:
• Items in the first column of the file are: Gene names and/or identifiers
• Data column(s) to use: 1-6
• Data values use a: 0-centered scale
• Select type of values: Relative
• Choose a color scheme: Full color spectrum with a maximum cut-off
• Maximum cutoff is: 1.2
• For relative data values use: No ratio of data columns

AraCyc Omics sample file 2

This file contains 1 column that represents relative levels of metabolite expression compared between two samples. There are no negative values. Data values between 0 and 1 indicate a relative decrease in expression levels.

• Items in the first column of the file are: Compound names and/or identifiers
• Data column(s) to use: 1
• Data values use a: 1-centered scale
• Select type of values: Relative
• Choose a color scheme: Full color spectrum from data
• For relative data values use: No ratio of data columns

PoplarCyc Sample Data Files

PoplarCyc Omics sample file 1

This file contains 4 columns that represent relative levels of transcript expression compared across different samples. There are no negative values. Data values between 0 and 1 indicate a relative decrease in expression levels.

• To view the first data point:
• Items in the first column of the file are: Gene names and/or identifiers
• Data column(s) to use: 1
• Data values use a: 1-centered scale
• Select type of values: Relative
• Choose a color scheme: Full color spectrum from data
• For relative data values use: No ratio of data columns


• To view the all time points in an animation:
• Items in the first column of the file are: Gene names and/or identifiers
• Data column(s) to use: 1-4
• Data values use a: 1-centered scale
• Select type of values: Relative
• Choose a color scheme: Full color spectrum from data
• For relative data values use: No ratio of data columns