Figure 15 of Geisert, Mol Vis 2009; 15:1730-1763.

Figure 15. Network graph makes highlights transcripts associated with Tyrp1 and Tyr. The 18 transcripts (nodes) in the graph are connected by Pearson correlation coefficients greater than 0.7 (red lines). How to define genetic networks in the eye: Step 1. Open either the main website GeneNetwork. Step 2. Set up the Find Records field to read “Choose Species=Mouse, Group=BXD, Type=Eye mRNA, Database=Eye M430v2 (Sep08) RMA. Step 3. Enter the search term “Tyrp1” in the ANY field and click on the 'Search' button. Step 4. Select ProbeSet/1415862_at to generate the Trait Data and Analysis form. Step 6. In the Analysis Tools section, locate the options for Trait Correlations. Under Choose Database select the Eye M430V2 (Sep 08) RMA database, under Return select top 100, and select 'Trait Correlations'. A Correlation Table is constructed listing the top 100 correlates associated with the Tyrp1 expression variation in the eye. Step 7. Click on as many as 100 of the correlates. For the graph above, we have specifically selected the first Tyrp1 probe set and the next 17 probe sets of the 100 genes that are of the most interest and highest correlation. After the probe sets are chosen, select the 'Add to Collection' function. Step 8. At the BXD Trait Collection page, select all or the genes of interest and select the 'Network Graph' function. For this figure an absolute value of 0.7 was set as the correlation threshold in the user defined settings. The network is drawn using certain default parameters that can easily be changed. The network displays are interactive and allow the user to link to interesting nodes and traits for further analysis.