© 2003-2011 Junior Research Group Integrative Transcriptomics.
Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen. All rights reserved.

Microarray Data Analysis
About Mayday Use Mayday! Documentation Contact
 

MGV FAQ

  1. How do I use MGV?
    Run MGV in three easy steps:

    1. Run Mayday
    2. Load a dataset (see here for an example dataset).
    3. Select a probe list, and choose “Probe List” -> “Visualization” -> “Graph Viewer” from the menu. MGV starts with the currently selected probe lists.
  2. How to import pathways into MGV
    In MGV, Graphs can be imported from and created from several sources. The “Create Graph” Wizard helps you with this:In the main menu, click on “Graph” -> “Create New Graph”. A five page Wizard shows up:

    1. Page 1: From the drop down menu, choose “BioPax Pathway”
    2. Page 2: Select a BioPax Level 2 file containing one or more pathways (you can select a pathway later)
    3. Page 3: From the tree on the left, select the” Complete Dataset” item from any dataset (e.g. Microarray + Metabolomics data) you want to use.
    4. Page 4: Select a Meta Information Group that has a mapping from probe names in Mayday the identifiers in the BioPax file.
    5. Page 5: Select a Pathway from the list.

    Opening Pathways in KEGG, SBML and other formats work essentially in the same way, simply choose the appropriate entry on page 1 of the “New Graph” wizard. Some pages of the wizard are not used during the import of these formats.

  3. How to view Gene Models
    Viewing Gene Models requires Locus Information to be available for each transcript. Such data can be imported via Mayday SeaSight.

    1. In Mayday, select a Probe list that corresponds to a gene with several transcripts.
    2. Open this ProbeList in MGV.
    3. Select “View” -> “GraphProvider” from the main Menu of the MGV window.
    4. Select “Gene Models” from the drop down menu in the dialog and answer the next question with “Ok”.
    5. A dialog with several fields shows up:
      (1) Locus Mapping: The gene loci meta information.
      (2) Style: The style of the graph. Either a Verbose, Simplified or Compressed style can be used.
      (3) Scaling: Controls the size of the exons. The “Scale Exon Height” option increases the size of nodes representing exons that are part of more than one gene model.
      (4) Exon Level Data. If exon level data is available, an additional dataset with gene locus mapping can be selected.
    6. Check the values in this dialog, especially the style and scaling options.

    After confirming your settings, the splice graph is created.

  4. Additional Plugins
    See this page on how to add additional layout  features.
  5. Problems with BioPax Graph Import
    The BioPax import option (Create Graph… BioPax) which allows to create overview graphs of BioPax files, and some other import plugins require the SQLite library to run. Download the SQLite jar file from here (direct download) and place it into the “additionalPlugins” folder. Then, everything should work fine.

More about MGV