Sex-related differences in gene expression in salivary glands of BALB/c mice

The following tutorial walks through the analysis results presented in:
Treister N.S., Richards S.M., Lombardi M.J., Rowley P., Jensen R.V., Sullivan D.A. Sex-related differences in gene expression in salivary glands of BALB/c mice J Dent Res. 2005 Feb;84(2):160-5.

When you are ready to begin this hands-on tutorial, click the second button down on the right, labeled "Log in to the dataset with tutorial."

1. Select Pairwise in the menu bar on the left side of the screen labeled Control Panel. You will see “Pairwise” under the heading marked “Analysis.”

2. Select the magnifying glass icon next to “Mouse 10K” in the list. The data presented here was generated using the CodeLink Uniset I 10K Mouse array. There are approximately 10,000 transcripts represented on this array.

3. This example will compare gene expression in submandibular glands from male mice with glands from female mice. There are three replicates for each of the two groups in this study. Select the three male SMG samples ("SMG M") to place them in Group 1.

4. Select the three female SMG samples ("SMG F") for Group 2.

5. Pairwise analysis combines a fold-change cutoff with a quality filter and comparison statistics to generate a list of differentially expressed genes. Select the following settings:

Normalization: None
Data was normalized using CodeLink software and then loaded into GeneSifter.

Statistics: t-test
Performs a two-sample, unpaired t-test for each gene that passes the quality and fold-change cutoffs.

Quality: 0.75
Will filter out low intensity spots.

Threshold: Lower = 1.5; Upper = None.
Filters out genes with less than a 1.5 fold change in expression.

Correction: None
No correction will be performed.

Data transformation: No transformation
Data will not be logged.

6. Select the Analyze button.

Note: This tutorial walks through the analysis used to generate figure 2 (Treister et al. J Dent Res. 2005 Feb;84(2):160-5). Changing the threshold and selecting other samples will generate the data used for figure 1.

7. After the analysis is performed a gene list will be returned. The Pairwise Analysis Results Page lists the genes that are differentially expressed based on the pairwise analysis settings selected. 464 genes passed the filtering criteria.

8. To view data and a gene summary for any gene in the list, click the Gene Name.

9. This will bring up a data summary and a One-Click Gene Summary™ (OCGS) for the gene. The One-Click Gene Summary provides a synopsis of current UniGene and Entrez Gene (formerly known as LocusLink) information for the gene.

10. Go back to the gene list by clicking the “Back” button in your browser.

11. Select the Ontology link at the top of the screen to view a summary of the Gene Ontology terms associated with the genes in the list. See the online help system for information about the other reports.

Note: To the view page-specific online help documents for any page, select the question mark icon located in the upper right corner of each page.

12. The Ontology Report lists the Gene Ontology terms associated with the 464 genes in the pairwise results gene list. See the help documents for this page for more information about the Ontology Report.

15. Click on Z-score report in the upper right corner of the Ontology Report window.

16. The z-score report lists the biological process ontologies that are significantly over or under-represented in the gene list (z-score greater than 2 or less than -2, respectively). Select the red arrow in the z-score column (on the right of the screen) to sort the list by z-score for the up-regulated genes.

Note: Ontology reports can be generated for each gland by performing pairwiseanalysis for each set of glands and viewing the Ontology Report for each gene list.

Only a few specific aspects of the data set have been explored here. Feel free to examine the data further on your own.