GenMAPP Tutorials
  Getting started with GenMAPP
  Importing data to GenMAPP
  Visualizing data on pathways
  Drawing a pathway
  Using MAPPFinder
  Submitting a pathway MAPP to WikiPathways
  Creating publication-quality figures in GenMAPP

Importing Data to GenMAPP

Prerequisites

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 a set of typical pre-processing steps which does not represent a solution for all datasets.

Background adjustment, normalization and probe-level summarization

Background adjustment and normalization algorithms are typically included in array image processing applications, so these algorithms may be applied to your data by the core lab or facility that processes the arrays. Similarly, summarizing the data at the level of probes (for Affymetrix arrays) is commonly done at this stage as well, before the data reaches the end user. Since there are many algorithms available that will all have different effects on the data, consulting a statistician in regards to your specific dataset is advised.

Combining all data in one spreadsheet

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.

Combining data into one spreadsheet

Calculate metrics

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.

Formatting the data

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.

  1. Open the file containing all data in Excel.
  2. Make sure each row of the first column contains a GenMAPP-supported ID.
  3. Insert a new column as the second column. Label the column "System Code".
  4. Fill the second column with the appropriate System Code for the ID contained in column 1.
  5. Make sure each column header does not include illegal characters.
  6. Make sure no column headers are duplicated.
  7. Delete any commas contained in any of the columns by using the Find and Replace function in Excel.
  8. Save the file as a .txt or .csv file.

Formatting data for import to GenMAPP

Importing the data

Once the data is properly formatted, it can be imported to GenMAPP via the Expression Dataset Manager:

  1. Download the appropriate database in GenMAPP.
  2. Load the appropriate Database in GenMAPP under Data>Choose Gene Database.
  3. In the Expression Dataset Manager, select File>New to begin the data import process. For details on data import, please refer to the Expression Dataset Manager.
  4. In the Data Type Specification window, make sure only those fields containing text or a combination of text and numbers are checked.

Importing data using the Expression Dataset Manager

Creating coloring criteria

To create Color Sets for your dataset, use the Criteria Builder in the Expression Dataset Manager. For detailed instructions, see Expression Dataset Manager.

  1. In the Expression Dataset Manager, select Color Sets>New.
  2. Type in a name for the Color Set.
  3. From the Gene Value drop-down, select a parameter value to be displayed to the right of each gene box on the pathways.
  4. In the Label in Legend field, type in a name for the first criterion.
  5. Select a color by clicking the Color box.
  6. In the Criterion field, type in your criteria by selecting parameters from the Columns list and operators from the Ops list.
  7. Click Add to add the criterion to the list.
  8. Repeat steps 4-7 for each additional criterion.
  9. Organize the order of the criteria using the Move Up and Move Down buttons in the Criteria List. Click here to find out why the order of criteria is important.
  10. When you are finished with the Color Set, click the Save button.
  11. Repeat steps 1-10 for additional Color Sets.

Creating Color Set in the Expression Dataset Manager

Do you have comments or questions about this tutorial? Contact GenMAPP Support.