GenMAPP 2.1 allows for simultaneous display of multiple coloring criteria on MAPPs. This "striped gene" feature was designed to help in interpretation of complex data and to allow for more innovative and complex visual display options. With this feature, it is possible to display any number and combination of criteria at one time, for example displaying multiple time points in a time course or displaying different types of data together, such as gene expression and proteomic data.
The striped gene view can be applied to any dataset which contains multiple Color Sets. The user defines which of the Color Sets to display, and each Color Set selected creates a horizontal stripe in the gene box. The below figure attempts to visualize the relationship between stripes and Color Sets.
Note: Each stripe is equivalent to one Color Set and therefore a set of criteria, not a single criteria.
GenMAPP analysis requires that the raw data is pre-processed into a form that can be used by GenMAPP. Pre-processing typically includes things like background adjustment, normalization and probe-level summarization, but since each experiment is unique it is not possible to make recommendations as to exactly what type of pre-processing should be done. Because of this, the below instructions list set of typical pre-processing steps which does not represent a solution for all datasets.
For the purpose of these instructions, an example dataset is used. The data is from Griffin et al. (Mol Cell Proteomics, 2002) and investigates the effects of carbon-source perturbation in Saccharomyces cerevisiae, in terms of both gene expression and protein levels. Yeast was grown on either galactose or ethanol, and RNA and protein was harvested. cDNA from the RNA was assayed on custom arrays measuring 6200 yeast ORFs and protein quantitation was carried out by ICAT analysis.
Any type of metric or parameter can be used to color genes in GenMAPP, including text-based parameters. Calculating the metrics can be done in several ways, for example programmatically, in a database program or most commonly in Excel.
Example data: Both gene expression values and protein levels were provided as a supplemental table was used as a starting point for GenMAPP analysis. For both data types, the log10 ratio of abundance on galactose vs. ethanol was provided.
To use GenMAPP, the complete dataset (all arrays) must be contained in one file. If the data is not immediately available in this summary format, all relevant files must be combined. Most often this means combining separate data files containing data for individual arrays into one file, but it can also mean combining different types of data.
Example data: The data was available as a supplemental table containing both data types.
Before import to GenMAPP, the data needs to be formatted according to GenMAPP specifications. Briefly, this includes adding a System Code column containing a system code for each entry and organizing the columns to have a GenMAPP supported ID in the first column and the System Code as the second column. For details on how to do this, see the Expression Dataset Manager.
Example data: Yeast ORF IDs in the original data table were substituted with SGD gene IDs as primary ID. A System Code column was inserted as the second column, and filled with the System Code for SGD (S).
Once the data is properly formatted, it can be imported to GenMAPP via the Expression Dataset Manager:
To create Color Sets for your dataset, use the Criteria Builder in the Expression Dataset Manager. While the process of creating Color Sets is the same for all GenMAPP datasets, creating Color Sets for the specific purpose of simultaneous visualizing of multiple Color Sets requires some additional considerations:
Example data: Two Color Sets were created, one for gene expression and one for protein levels. The same fold change cutoffs were used in both Color Sets for up- and down-regulation:
When the dataset contains the Color Sets you want to use for simultaneous display, selecting them for display is straightforward. First, load the appropriate database in GenMAPP, and open a pathway of interest.
Selecting multiple Color Sets for display is done in the Color Set drop-down list. Select relevant Color Sets for display in the Multiple Color Sets window by Ctrl+click or click the All button to select all Color Sets. For example, if you two data types each with one Color Set, you should select both of these Color Sets for display. For detailed instructions on how to select multiple Color Sets, see the Drafting Board Toolbar.
Example data: Both Color Sets described above were selected for display, resulting in each gene rectangle being split in half between data for gene expression and protein levels.
Note: Depending on how many Color Sets you choose for display and how complex these are, coloring the pathway may take a few seconds.
For the striped gene view, the Legend displays which Color Sets are currently displayed for which stripe of the gene, and what each color represents. The coloring legend can be displayed for the first Color Set only or for each Color Set. This behavior is controlled in the Options menu. For readability, it may be convenient to display the Legend for only the first Color Set, if many Color Sets are selected for display and if they all share a similar color scheme. For details on this please refer to the Legend.