An Expression Dataset is a GenMAPP-created file with the extension .gex; for example MyExperiment.gex. Expression Datasets may be imported into GenMAPP from data produced by your own experiment. The Expression Dataset consists of several different components:
Expression Datasets are independent of MAPPs and applied dynamically to them. One MAPP, then, can have any number of Expression Datasets applied to it and one Expression Dataset may be applied to any number of MAPPs.
An Expression Dataset may contain any number of Color Sets, instructions to GenMAPP on how to color and display data on gene objects in a MAPP. Each Color Set contains a set of criteria, each with a different color. When the expression data for a gene meets a criterion, it is colored with the color associated with that criterion. For example, a Color Set's criteria may direct GenMAPP to color all genes up-regulated by a certain amount red, and all genes down-regulated blue. The data value that is displayed next to gene rectangles on your MAPPs is called the gene value; the specification for the column of data the gene value is derived from is part of the Color Set.
Color Sets are applied to MAPPs dynamically. When viewing a MAPP, you may switch Color Sets at will by choosing from the Color Set drop-down selection list on the Drafting Board Toolbar. You can easily switch between Color Sets to see what genes change with different fold cut-offs, for example. Multiple Color Sets can also be displayed simultaneously on a MAPP, facilitating visualization of data from different disease stages or time points during an experiment.
Color Set Criteria can be quite sophisticated. For example, you may wish to color genes red that exhibit a fold change of 2 to 4 at a 2-week time point and orange for a greater-than-4 fold change at the same time point, with the further qualification that both expression values have a P value less than 0.05. If the data exists in the Expression Dataset, your criteria can be made to react to it.
Expression data are applied to gene objects by coloring the gene according to the Color Set criteria satisfied and displaying a value next to the gene. The value is from a column in the Expression Dataset that you choose when editing a Color Set in the Expression Dataset Manager.
When you launch the GenMAPP Program, the gene objects on the first MAPP you open will be white because they have not yet been colored with an Expression Dataset. You can color the gene objects by choosing Data > Choose Expression Dataset, from the menu at the top of the Drafting Board window. You may switch between different Color Sets for the same Expression Dataset by selecting a different Color Set from the drop-down list in the Drafting Board Toolbar. Each time you choose a Color Set, GenMAPP automatically applies the expression data to the gene objects according to the Criteria you have set in the Expression Dataset Manager. Once you have chosen an Expression Dataset and Gene Color Set for viewing, each subsequent MAPP that you open in the same session will be colored with that same Expression Dataset unless you select another Expression Dataset or choose No expression data from the drop-down menu.
You also have the option of having GenMAPP open already displaying an Expression Dataset. To activate this option, go to the Tools menu and choose Options... Choose the Coloring tab and check the box next to Always open GenMAPP with the most-recently-used Expression Dataset loaded.
Each gene object on a MAPP is identified with an identifier from a gene ID system in the underlying Gene Database and the System Code for that gene ID system. For example, the MGI:98834, M for an ID from Mouse Genome Informatics. GenMAPP can associate gene expression data with that gene object in two different ways:
In this scheme, GenMAPP matches the gene object's identifier to all genes in your Expression Dataset that are related to that gene identifier as determined by the relationships established in your Gene Database. For example, if the gene object on your MAPP is identified as MGI:98834, GenMAPP may search the relational data in your Gene Database to discover that MGI:98834 is directly related to Entrez Gene 22059, as well as UniProt P53_MOUSE, and Unigene Mm.222. All rows in your Expression Dataset that have any of these identifiers are used to determine the gene object's color and value. This is the default coloring option for GenMAPP because it takes maximum advantage of the gene ID relationships in the Gene Database.
GenMAPP looks for data in your Expression Dataset that exactly matches the gene ID and gene ID system of the gene object being colored on the MAPP. For example, if the gene object on your MAPP is identified as MGI:98834, GenMAPP uses only rows in the Expression Dataset that are identified as MGI:98834.
You can choose the type of association from the Drafting Board window by left-clicking on the Tools menu, choosing Options…, and clicking the Coloring tab.
Your Expression Dataset may contain multiple rows of data that correspond to the same gene object. This may occur under two conditions: First, the same gene identifier may occur in more than one line of data, as is the case when multiple spots on an array contain DNA from the same gene. Second, the gene identifier may be related to another one as determined by the relationships established in your Gene Database. Each of these rows may have different data values that satisfy different Color Set criteria. When applying a color to a gene object, GenMAPP first assembles all the relevant rows of data in the Expression Dataset, and then determines which criterion is satisfied by each row. GenMAPP calculates the mode criterion, that is, the criterion satisfied by the greatest number of records, and uses that criterion to color the gene. The gene value displayed next to the gene rectangle is from the first row of data satisfying that criterion.
Gene objects that have more than one line of data in an Expression Dataset associated with them are represented on a MAPP by having a dashed line around the gene rectangle. If the gene rectangle with a dashed line is filled with a solid color, each of the lines of data for that gene satisfied the same criterion.
If the gene rectangle with a dashed line is filled with two different colors (a central color and a rim color) that means that two different lines of data associated with that gene object meet different criteria in the Color Set. The rim color is the second most frequently met criterion. Left-click on a gene rectangle on a MAPP to open the Backpage and view all the data along with the corresponding gene identifications.
The order of the data in your Expression Dataset was assigned when the raw data file was imported and has significance to the Expression Dataset Manager. It is used to break ties. If two criteria are tied (e.g., each is met by four occurrences in the data) the criterion that was met by the earlier-occurring row of data is used to color the gene. In addition, the value displayed next to the gene is that from the row of data occurring first for that coloring criterion.