From OpenTutorials
Jump to: navigation, search
This tutorial is still under construction.

This tutorial outlines analysis of time-course expression data in GenMAPP-CS. The example data used is a subset of a microarray experiment examining mouse myometrium during pregnancy. The data is available here and has been described here.

To download GenMAPP-CS, please visit our website.

Loading data

The MusMusculus_Affy_9762-Salomonis.txt file contains Affymetrix array data for non-pregnant controls (NP), 4 time points throughout gestation (14, 16, 17 and 18 days) and two time points postpartum (6 and 24 hours).

There are multiple columns for each time point:

avg: Group average expression
log-fold: log (base 2) fold change as compared to NP controls.
t-test: p-value for the "log-fold" comparison
-log fold: log (base 2) fold change as compared to the 14 day time point, for example "16v14-log fold".
  • In the Database panel of Workspaces, select the mouse database, since the data for this tutorial is from mouse myometrium tissue. Detailed instructions on how to select a database are available in the Expression Analysis tutorial.
  • Import the data file under Import dataset from table... in the Actions menu. For detailed instructions on how to use the GenMAPP-CS Dataset Import, refer to the Expression Analysis tutorial.

dataset import

Creating coloring criteria

We are going to create 6 criteria sets, one for each gestational time point (14, 16, 17 and 18 days) and postpartum time point (6 and 24 hours). Each criteria set will contain criteria for up- and down-regulation, as compared to either controls (for the 14 day time point) or the 14 day time point (for all other comparisons).

Below are two examples of how the criteria should be setup. Note that the criteria in the two different sets are identical, except for the data column used. Keep in mind that the data used is log fold values, while the labels indicate the fold change in normal space, for better readability.

14 days vs control
2 fold up: 14days log-fold > 1 → bright red
1.5 fold up: 14days log-fold > 0.6 → light red
2 fold down: 14days log-fold < -1 → bright blue
1.5 fold down: 14days log-fold < -0.6 → light blue
16 days vs 14 days
2 fold up: 16v14-log fold > 1 → bright red
1.5 fold up: 16v14-log fold > 0.6 → light red
2 fold down: 16v14-log fold < -1 → bright blue
1.5 fold down: 16v14-log fold < -0.6 → light blue

To create multiple criteria sets that are all similar, like in the case of time-course data, it is convenient to copy an existing criteria set and then altering the rules and/or colors.

  • Create the first criteria set, for the "14 days vs control" comparison. Click Save.
  • To copy the criteria set, simply click the Duplicate button. Enter a new criteria set name, and click Enter to continue. For the purposes of this tutorial you can now easily edit the criteria by first selecting the criteria in the Criteria list, then in the Expression Editor, change which attribute is used. You can use this same strategy of copying and editing for the remaining criteria set.

Below is an example of what the two criteria sets above would look like in the Criteria Builder.

criteria builder time course criteria builder time course

  • When you have created all the criteria sets for the time course, click Save, Apply and then Close.

Loading Networks

For the purposes of this tutorial, we will load the "Prostaglandin Synthesis and Regulation" pathway from WikiPathways, using the WikiPathways search interface. To find this pathway, use the search term "prostaglandin".

  • To load a network from WikiPathways, select Load network from web... from the Actions drop-down. This brings up an interface for importing networks from the WikiPathways web service.
  • Select the appropriate species in the organism drop-down.
  • Type in your search term in the Search field.
  • Search results will be displayed as a list. Simply double-click on any entry to open the network.
  • To make it easy to load additional networks, the WikiPathways web service interface will remain open until you decide to close it.

Viewing time-course data on networks

The Prostaglandin pathway will be colored according to the last criteria set created. This may vary depending on the order you created the criteria set in, but may look something like this:

prostaglandin pathway

  • To view all color sets on the pathway simultaneously, right-click on any of the criteria sets in the Criteria Set panel of Workspaces and select Combine All Criteria.

This will create one vertical colored stripes on network nodes, each stripe representing a criteria set.

pathway with time course data

Note: The ordering of the vertical stripes currently doesn't correspond to the order of criteria sets in the Criteria Set panel of Workspaces. This feature is still under development.